Exome Analysis


Whole exome sequencing involves capturing the coding region of the genome, or exons (EXpressed regiONS). SNVs and indels are the most important and abundant types of variation in exons. Several variant calling programs have been developed for whole exome sequencing. New strategies to reduce false positive and false negative rates are some of the most important challenges. Exome sequencing analysis can be divided into several steps:

  1. Base calling and image analysis
  2. Gapped alignment
  3. Sorting, indexing and PCR duplicate removal
  4. SNP calling
  5. Annotation

A final visualization of SNP data can be made using IGV: http://www.broadinstitute.org/software/igv/ or a number of other tools. Visualization makes identifying sequencing artifacts versus true variants easier and allows for easy comparisons between data sets.

Providers offering Exome Analysis (found 38)


Geno-plex Bioinformatics Services

Switzerland

We offer tailored bioinformatics services (mainly NGS data analysis) to academic and private organizations. We have a strong academic background with a focus on cutting edge, open source software.

We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses independently.

We replicate recommended analysis pipelines (best practice) or develop novel ones but we always emphasize biological interpretation of your data.

Years in service: 11

Other services offered by Geno-plex Bioinformatics Services:

Service Description Price
Transcriptome Mapping We replicate recommended analysis pipelines (best practice) or develop novel ones according to your specifications using open source software. We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses ind… $150.00 USD (per sample)
Custom scripting and special projects We replicate recommended analysis pipelines (best practice) or develop novel ones according to your specifications using open source software. We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses ind… Inquire
Other Services Primer design for efficient multiplex PCR reactions Inquire
Exome Analysis We replicate recommended analysis pipelines (best practice) or develop novel ones according to your specifications using open source software. We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses ind… $150.00 USD (per sample)
Genome Mapping We replicate recommended analysis pipelines (best practice) using open source software. We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses independently. Inquire
SNP / Indel Calling We replicate recommended analysis pipelines (best practice) or develop novel ones according to your specifications using open source software. We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses ind… $150.00 USD (per sample)
SNP/SV/CNV Discovery We replicate recommended analysis pipelines (best practice) or develop novel ones according to your specifications using open source software. We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses ind… $150.00 USD (per sample)
Targeted Capture Analysis We replicate recommended analysis pipelines (best practice) or develop novel ones according to your specifications using open source software. We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses ind… $150.00 USD (per sample)
Variant Annotation We replicate recommended analysis pipelines (best practice) or develop novel ones according to your specifications using open source software. We build up your in house bioinformatics capacity in 2 ways: First, we provide you with the code underlying the analysis you requested. Second, we can help you to set up (cloud) computing solutions that will allow you to run and extend your analyses ind… $150.00 USD (per sample)

Parseq Lab

Czechia

Parseq Lab is experienced in: - massively parallel sequencing data analysis - client-tailored algorithms and software development - analysis pipelines deployment

We offer: - whole genome/exome and targeted sequencing data analysis - de novo assembly - SGV detection and annotation - expression analyses - metagenomics analysis - transcriptomics analysis - proteomics research - genuine task-specific workflows design - custom bioinformatics applications development - statistical data analysis

Collaborations: genomic research labs, sequencing facilities, academic and research institutions.

Years in service: 13

Other services offered by Parseq Lab:

Service Description Price

Cambridge Cancer Genomics

United Kingdom

CCG has developed precision oncology solutions for robust genomic data analysis.

Our OncOS platform offers data analysis in a rapid, scalable and secure manner. It provides comprehensive tumour profiling and reports actionable molecular insights to enable the delivery of a personalised treatment strategy for each patient.

Ultimately, we will ensure that each patient has the right treatment, at the right time, to beat their cancer.

  • Variant calling
  • Variant alignment
  • SNVs
  • MSI
  • TMB
  • CNVs
  • INDELs
  • Drug matching
  • Clinical trial matching

Other services offered by Cambridge Cancer Genomics:

Service Description Price
Exome Analysis We use a neural network-based variant caller for accurate detection of variants in the tumour sample. Exome analysis includes quality control, alignment, variant calling, variant annotation and actionable information (available therapies and clinical trials). * Germline variants, compared to reference genome * Somatic mutations - require Tumor-Normal pair (SNVs, INDELs, CNVs, MSI, TMB) $100.00 USD (per sample)

Lifecode Technologies

NGS provider India

Lifecode Technologies is a Private Limited company incorporated in the year 2013 and backed by a bunch of passionate genomic scientists with the aim to offer reliable genomic solutions to improve lives. The company was formed to realize the passion of its founders to deliver reliable, scientifically backed , state-of-the-art and cost-effective diagnostic solutions to physicians and care-givers, and fill in the unmet gap in translation of genomic technologies from bench to bedside.

We provide advanced data analysis services encompassing a complete range of NGS applications, ranging from Exome/Whole Genome Sequencing, Denovo Assembly Transcriptome/RNAseq Analysis, ChIP-seq and Bisulfite-Seq/WGBS Analysis. We also deelop NGS based panels for Diagnostic Applications

Other services offered by Lifecode Technologies:

Service Description Price
Exome Analysis $500.00 USD (per sample)
ChIP-Seq Analysis $500.00 USD (per sample)

Varstation

Brazil

We offer a solid bioinformatics foundation for laboratories that want to start or scale their capacity to perform genetic testing while following the best practices from ACMG, AMP and CAP.

End-to-end and automated processing Evaluation of quality parameters, mapping, multiple variant callers, database annotation and automatic pre-classification according to ACMG and AMP guidelines.

Support for clinical interpretation More than 200 genetic mutations databases are incorporated, including data for germline, somatic and structural variants (CNV and Fusion).

Robust filters Filtering engine based on all annotated mutation data, including human phenotypes, the patient's clinical history and diseases (OMIM / UniProt).

Clear and structured results Relevant clinical information to support the medical report, such as patient, variants and therapies info. We provide a Datavis feature to share results with partners.

Years in service: 9

Other services offered by Varstation:

Service Description Price
Exome Analysis Exome analysis inside Varstation using the gold standard methodologies, including disease and HPO correlation and filtering. $65.00 USD (per sample)
SNP / Indel Mapping End-to-end tool, from the sequencing raw file to the variant report $30.00 USD (per sample)
SNP / Indel Calling End-to-end tool, from the sequencing raw file to the variant report $30.00 USD (per sample)
SNP/SV/CNV Discovery Complete CNV processing from sequencing data to final report using know CNV baseline $30.00 USD (per sample)
Variant Annotation Variant annotation using multiple VCF callers for any pipeline using our annotation algorithm that includes more than 200 genetic mutations databases, $30.00 USD (per sample)

Quick Biology Inc.

NGS provider United States of America

Quick Biology Inc. is a CLIA-certified startup biotechnology company located in Monrovia, CA. QB has a fully automated, high-throughput genomic center equipped with all major next-generation sequencing. QB provides state-of-the-art genomics technologies, comprehensive services, and specialized expertise to enable our services in a cost-effective and timely manner to serve basic science and translational/clinical research.

We also help physicians to unleash the power of NGS in disease diagnosis. (U.S. Federal CLIA#: 05D2286116; California State CLIA ID: CLF-90009922)

★We are equipped with the latest Illumina NovaSeq X Plus, NovaSeq 6000, HiSeq X Ten, HiSeq 4000, NextSeq500, MiSeq and Ion Proton.

We have --High sequencing throughput and capacity (NovaSeq 6000 S2 flow cell, ~3300M reads of PE150) --Fast turnaround time (our NovaSeq runs once a week and Hiseq X runs twice a week on a routine basis) --Very competitive price in RNA-seq and Whole Exome Seq --Advanced bioinformatic analysis, including analysis for RNA splicing/RNA editing -- High-quality pictures for publication purposes

★We also provide functional genomic screening service using our proprietary Drug Array and siRNA Array to conduct functional studies on your pathway of interest through drug-drug and drug-gene interactions on your cell line of interest. (1) Drug Array: - This Drug Array comprises 66 highly selective anti-cancer drugs, which allows users to quickly screen potential drug-drug and drug-gene interactions. It serves as a great tool to survey synthetic lethality for cancer treatment. It also serves as a tool to probe pathway-pathway interactions. (2) siRNA Array - siRNA array for Drug Targets: This array set silences 60 well-known drug targets, which allows users to screen potential gene-gene and gene-drug interaction. - siRNA array for Cancer Driver Genes: This array set silences 60 well-known cancer driver genes.

Years in service: 10

Other services offered by Quick Biology Inc.:

Service Description Price
Differential Gene Expression Analysis $100.00 USD (per sample)
Exome Analysis Whole Exome Sequencing analysis: a.Germline variants, compared to reference genome b.Somatic mutations if Tumor-Normal pair (SNVs, InDel, CNV) c. Pathway Analysis of Variants d. Interaction Network Analysis of Variants $170.00 USD (per sample)
ChIP-Seq Analysis ChIP Sequencing analysis: a.Raw data QC and clean up b.Alignment to a reference with mapping statistics c.Peaking calling with or without control samples d.Gene assignment and peak annotation e.Visualization f.Final project report with analysis methods, publication-ready graphics, and references 120.00

Admera Health Biopharma Services

NGS provider United States of America

Admera Health is an advanced molecular diagnostics and research service provider. Utilizing genomic and proteomic technology platforms (such as next generation sequencing and aptamer), together with advanced bioinformatics, Biopharma Services of Admera Health seeks to redefine the delivery of transformative, valuable solutions for all researchers and biopharma companies.

Biopharma Services of Admera Health operates in a CLIA-certified and CAP-accredited laboratory for the development, validation, and delivery of proprietary laboratory developed tests (LDTs) as well as RUO (Research Use Only) services. We are committed to maintaining compliance with all clinical regulations and to upholding the highest quality standards for all our projects.

Please follow the link for more information: https://www.admerahealth.com/genomics-and-bioinformatics-2/

Years in service: 12

Other services offered by Admera Health Biopharma Services:

Service Description Price
Differential Gene Expression Analysis We provide full bioinformatics service from experimental design to RNA-Seq data analysis and statistical modeling, as well as GO/Pathway enrichment analysis Starting at $50 $50.00 USD (per sample)
Exome Analysis Our bioinformatics pipeline supports standard analysis from raw data quality assessment to variant annotation and any further customized analysis Starting at $75 $75.00 USD (per sample)
ChIP-Seq Analysis Our robust ChIP-Seq analysis pipeline includes raw data QC and clean up, reads mapping, differential binding analysis, peak calling and annotation, motif analysis, GO/pathway enrichment analysis $75.00 USD (per sample)

BioInfoRx

United States of America

At BioInfoRx, we help scientists obtain biological insights from complex genomic data. We provide complete NGS analytic solutions including standard analysis of raw data, integration between multiple experiments, and online database for data mining and visualizations. We use best-practice open source tools to analyze your raw NGS data, and provide meaningful annotations and downstream data mining tools to help you infer functional insights.

As demonstrated by the numerous publications using our services or web-bases tools, our biology-centric approach has proven effective to decipher molecular mechanisms from genomic data.

Years in service: 15

Other services offered by BioInfoRx:

Service Description Price
Differential Gene Expression Analysis We use a robust pipeline with flexible statistical models to identify differentially expressed genes (DEG) from raw RNA-Seq data. The list of DEG is only part of the results we delivery. We also help you assess data quality and verify your experimental design, and deliver your data in an online database where you can perform additional data mining: 1) Adjust filter criterion for DEG 2) Search f… $99.00 USD (per sample)
Custom scripting and special projects We offer a variety of custom genomic analysis services. Our team has both strong biological and computational background, and we can tackle any questions for you. -Custom genome browser -Online genomic database -Circo plots, pathway analysis -Functional annotation of newly sequences genomes -Integrative analysis of RNA-Seq, ChIP-Seq, motif discovery, etc. $125.00 USD (per hour)
Exome Analysis We use best-practice method to map reads and make variant calls. We include robust quality control metrics for exome capture performance. The variants come with rich annotation regarding effects on genes and regulatory regions. $99.00 USD (per sample)
ChIP-Seq Analysis Finally you can unleash the full potential of your ChIP-Seq data in a quick and easy way. With the biologist-friendly web interface powered by BxChIPSeq 2.0, you can focus on the biology without worrying about hardware, software, algorithms. -Peak Report (with gene annotations, and enriched genomic regions) -De novo motif discovery, and enriched known motifs -Functional enrichment of genes (G… $99.00 USD (per sample)
Targeted Capture Analysis We use best-practice method to map reads and make variant calls. We include robust quality control metrics for target capture performance. The variants come with rich annotation regarding effects on genes and regulatory regions. $99.00 USD (per sample)

Genotypic Technology

NGS provider India

Genotypic Technology is the first genomics company based in India with a state-of-the-art, ISO 9001:2008 accredited, SAP-enabled, 12,000 square feet facility in Bangalore. Our high-throughput facility enables us to offer customized services for experiment design consultation, protocol optimization, microarray and probe designing, next-generation sequencing (NGS), and bioinformatics solutions to clients from academia, biotech, and pharma sectors worldwide.

We have been providing high-quality sequencing services, including whole-genome sequencing (WGS), transcriptome sequencing, shotgun metagenome sequencing, and de-novo assembly since 2000. Our skilled team has experience in working with genomes of all sizes and nucleic acids from various sources on Illumina, Oxford Nanopore, and other platforms. We have developed targeted panels for various viruses like Adenovirus, KFDV, SARS-CoV-2, Dengue, and pipelines for predicting virulent strains that may be difficult to treat with conventional antibiotics.

Our broad range of metagenome services includes targeted and whole-genome metagenome and metatranscriptome sequencing. Our long amplicon metagenome approach provides the best resolution of microbes up to the sub-species level, while whole-genome metagenome sequencing enables the identification of gene clusters, resistome, and novel pathways in a given environment. We also specialize in Ribo-footprinting and RNA immunoprecipitation sequencing, ChIP sequencing, and targeted methylation sequencing.

Years in service: 26

Other services offered by Genotypic Technology:

Service Description Price
Differential Gene Expression Analysis Differential Gene expressions, SNP variants and annotations with known reference, SSR discovery $69.00 USD (per sample)
Transcriptome Mapping $25.00 USD (per sample)
Custom scripting and special projects Bioinformatics support for 1 day - includes skype/webex consultation with detailed report. 120.00
Read Filtering and Cleaning $2.00 USD (per sample)
Exome Analysis Exome analysis - from raw data to VCF files and annotations from dbSNP, 1000 genome, COSMIC, SIFT, Polyphen2 and more $45.00 USD (per sample)
ChIP-Seq Analysis $250.00 USD (per sample)
Metagenomic Analysis $25.00 USD (per sample)
Transcriptome de novo Assembly Denovo transcriptome assembly with differential gene expression values. $600.00 USD (per sample)
Whole Genome de novo Assembly $2900.00 USD (per sample)
Base Calling $20.00 USD (per hour)

TACGenomics

United States of America

TACGenomics has a team composed of bioinformatician, molecular biologist and computer scientist who are all at Ph.D. level. Our team has the experience of hundreds of NGS data analysis projects from all over the world. The mission of TACGenomics is to help our customer to solve the biological questions. After computation analysis completed by the bioinformatician, our molecular biologist will interpret the analyzed data carefully, provide more insight into your project and help the publication of the project in the high impact journal.

Years in service: 10

Other services offered by TACGenomics:

Service Description Price
Differential Gene Expression Analysis Differentially expressed genes were identified using the edgeR program. Genes showing altered expression with p < 0.05 and more than 1.5 fold changes were considered differentially expressed. Goseq was used to perform the GO enrichment analysis and Kobas was used to performed the pathway analysis. $50.00 USD (per sample)
Transcriptome Mapping The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15. TMM (trimmed mean of M-values) was used to normalize the gene expression. $50.00 USD (per sample)
Custom scripting and special projects $50.00 USD (per hour)
Exome Analysis Our team has successfully discovered a causal variant which lead to a mendelian disorder through analyzing 20 samples in three-generation family. The error rate of genotype we called in this family is only 0.2% which indicate that our pipeline detect all the SNV very accurately. $80.00 USD (per sample)
ChIP-Seq Analysis $80.00 USD (per sample)
Genome Mapping $50.00 USD (per sample)
Metagenomic Analysis $100.00 USD (per sample)
Methylation Analysis $100.00 USD (per sample)
Transcriptome de novo Assembly $100.00 USD (per sample)
Whole Genome de novo Assembly $1000.00 USD (per sample)
Microbiome Analysis $50.00 USD (per sample)

EarlyDx

NGS provider

EarlyDx is committed to providing cutting-edge non-invasive genomics technologies and best-in-class early disease diagnostics. Our proprietary cfDNA-based technologies, in combination with powerful AI algorithms, have shown great potential to transform non-invasive biomarker discovery, diagnostics, and precision medicine for almost any diseases, including cancers, aging, metabolic diseases, autoimmune diseases, imprinting diseases, and neurological diseases.

Our key cfDNA-based best-in-class technologies include:

  1. cfMethyl-seq: a powerful and cost-effective NGS solution to profile the cfDNA methylome
  2. cfSNV: a cutting-edge computational tool to accurately call mutations directly from blood
  3. cfTrack: for non-invasive monitoring of cancer MRD, recurrence, and evolution
  4. EarlyDx-Cloud: a comprehensive bioinformatics data analysis platform for liquid biopsy

Please check out our relevant publications in details: https://earlydx.com/technologies/publications/

Years in service: 2

Other services offered by EarlyDx:

Service Description Price

Next Generation Intelligence

NGS provider Italy

NGI is a platform for Next Generation Sequencing data analysis. We offer a wide range of bioinformatics tools and an experienced and professional collaboration service for any type of biological data analysis. We provide both standard and customized analysis, custom softwares and pipelines development and post-sequencing support. We'll enhance and make easier your discovery process.

Expertise:

Our expertise is in the epigenetics field in mouse and human organisms.

Infrastructure:

we will provide FTP access to our storage server to upload raw data and download analyzed data.

Other services offered by Next Generation Intelligence:

Service Description Price
Differential Gene Expression Analysis Inquire
Transcriptome Mapping Inquire
Custom scripting and special projects Inquire
Other Services Inquire
Read Filtering and Cleaning Inquire
Exome Analysis Inquire
ChIP-Seq Analysis Inquire
Small RNA Mapping Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Targeted Capture Analysis Inquire
Genome Annotation Inquire
Small RNA Annotation Inquire
Methylation Analysis Inquire
Transcriptome de novo Assembly Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Base Calling Inquire

ecSeq Bioinformatics

Germany

Bioinformatics solutions

ecSeq provides a variety of bioinformatics service packages suited for most everyday high-throughput sequencing experiments. We are particularly engaged in RNA-seq projects (trancriptomics, differential expression), ncRNA analysis (small RNA-seq, ncRNA annotation) and epigenome sequencing (bilsufilte and methylation analyses). Further bioinformatics solutions include SNP calling, variant annotation & prioritisation as well as development of customized algorithms.

Public workshops and eTrainings

We develop eTrainings and provide workshops for employee training in bioinformatics. Several times a year, we organize well-attended workshops on selected topics in next-generation sequencing data analysis. Test datasets are used for getting started in applying and developing bioinformatic tools.

Topics covered by our workshops include:

  • RNA-seq bioinformatics
  • Sequencing technolgies
  • Small RNA-seq data analysis
  • Genomic data visualization
  • Perl for bioinformatics
  • Programming in R

Expertise:

We have long experience in the development and application of bioinformatics methods to high-throughput sequencing experiments. These methods have been successfully applied in various experimental designs ranging from ncRNA and mRNA sequencing to genome/epigeome analyses. We have worked with sequencing data from humans, lifestock species (chicken, cow, turkey), plants and bacteria. Our employees are continuously involved in projects from national and international consortia, like the International Cancer Genome Consortium (ICGC) or the Leipzig Research Centre for Civilization Diseases (LIFE).

Infrastructure:

We have access to moderate computation resources allowing us to process ~120GB sequence data per week.

Other services offered by ecSeq Bioinformatics:

Service Description Price
Differential Gene Expression Analysis Inquire
Transcriptome Mapping Inquire
Custom scripting and special projects Inquire
Read Filtering and Cleaning Inquire
Exome Analysis Inquire
ChIP-Seq Analysis Inquire
Small RNA Mapping Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Small RNA Annotation Inquire
Methylation Analysis Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire

ContigExpress, LLC

United States of America

ContigExpress is the leading integrated genomics data service provider. We offer genomic project management, data analysis, and bio-IT consulting services. Our unique value to our clients lies in our deep understanding of both biology and informatics. From project consultation, bio-IT infrastructure implementation, to data analysis, our experienced scientists deliver not only cost-effective customized informatic solutions but also their expert insights.

Our team consists of Ph.D.-level computational biologists with extensive training and professional practice in bioinformatics and genomic research. We understand both your cutting-edge research and your informatics challenges. We enable you and your team to extract actionable information from the vast amount of genomic data in a cost-effective and timely fashion.

We at ContigExpress strive to deliver affordable expert genomic data solutions to researchers and clinicians. We place the utmost emphasis on information confidentiality, data security, and data integrity. Please schedule a complimentary project discussion with one of our expert bioinformaticians to discover how we can help you move your genomics research forward!

Years in service: 15

Other services offered by ContigExpress, LLC:

Service Description Price
Differential Gene Expression Analysis Following is a list of common analysis items for RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Gene and transcript-based quantitation, RPKM/FPKM-based quantitation, Raw hit count-based … Inquire
Other Services We are a professional bioinformatics service provider and we are happy to provide customized informatic solutions to your unique research and business needs. Please feel free to reach out to us to discuss how we can help you. Inquire
Exome Analysis Following is a list of common analysis items for Targeted Resequencing and Exome Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP… Inquire
ChIP-Seq Analysis Following is a list of common analysis items for ChIP-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Peaking calling with or without control samples 5) Gene assignment and peak annotation 6)… Inquire
Small RNA Mapping Following is a list of common analysis items for small RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC, adaptor removal, and size selection 3) Read characterization by mapping to a reference genome sequence, known RNA families (e.g., Rfam), and known micr… Inquire
Genome Mapping Following is a list of common analysis items for Whole Genome Resequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP/small indel char… Inquire
Metagenomic Analysis Following is a list of common analysis items for Metagenomics Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Sequence assembly 4) Biodiversity analysis and binning 5) Gene predication and functional annotation 6) Gene Ontology and path… Inquire
SNP/SV/CNV Discovery Following is a list of common analysis items for Whole Genome Resequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP/small indel char… Inquire
Targeted Capture Analysis Following is a list of common analysis items for Targeted Resequencing and Exome Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Alignment to a reference with mapping statistics 4) Local realignment 5) SNP and small indel calling 6) SNP… Inquire
Genome Annotation Following is a list of common analysis items for Genome Annotation. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Gene prediction with or without RNASeq data 3) BLAST-based gene function annotation 4) Written project report with analysis methods, publication-ready graph… Inquire
Small RNA Annotation Following is a list of common analysis items for small RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC, adaptor removal, and size selection 3) Read characterization by mapping to a reference genome sequence, known RNA families (e.g., Rfam), and known micr… Inquire
Methylation Analysis Following is a list of common analysis items for Methylation Sequencing, including MeDIP-Seq, hMeDIP-Seq, RRBS / Targeted Bisulfite-Seq, WGBS, and 5-mc RNA-Seq. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Methylation state-sensitive mapping 4) … Inquire
Transcriptome de novo Assembly Following is a list of common analysis items for De Novo Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Transcriptome assembly, scaffolding and gap closure 4) Gene annotation (molecular function, Gene Ontology and pathways) 5) SNP disc… Inquire
Transcriptome Annotation Following is a list of common analysis items for De Novo Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Project consultation 2) Transcriptome annotation (molecular functions, Gene Ontology and pathway) 3) Written project report with analysis methods, publication-ready graphics, and references Inquire
Whole Genome de novo Assembly Following is a list of common analysis items for De Novo Sequencing. One of our expert bioinformaticians will work closely with you to identify a custom analysis workflow most appropriate for your project. 1) Experiment design consultation 2) Data QC and clean up 3) Contig assembly 4) Scaffolding and gap closure 5) Gene/ORF prediction 6) Gene annotation and classification via database search and… Inquire

Inocras Inc.

NGS provider
  • End-to-end diagnostics services featuring whole genome sequencing - for clinical applications of cancer, rare disease and MRD. Below are the listed applications for research:

Biopharmaceuticals and biotechnology --- Identify candidate biomarkers that correlate with outcomes Understand responders vs. non-responders during or post clinical trials Accelerate clinical trial enrollment by identifying patients for rare indications Analyze clinical trial results for efficiency and safety profile Leverage genetic information for label expansion with real world data Provide genetic testing for patient support program

Biobanks, research organizations and labs --- Research genomic profiles in-depth, often resulting in new biomarker identification, or re-classification Profile genomic characteristics of the acquired biospecimen to increase the value of your biospecimen assets

Health technology --- Leverage genetic information to provide precision health insights to your customers and users Generate real world evidence data including genetic information

Years in service: 1

Other services offered by Inocras Inc.:

Service Description Price

Station X

United States of America

We offer a powerful genomics software platform that makes various bioinformatics tasks fairly straightforward to perform and deliver to customers. We also wrap this product with various service offerings for folks interested in one-off projects that deliver results rather than just subscribing to a software solution and then do the work themselves. We are comfortable with both scenarios. We are well versed in working with RNA-Seq, Genomes, Exomes, targeted panels, miRNA-Seq, Copy Number, Gene Expression, Protein Expression, and DNA Methylation from the level of raw sequencing reads or chip data all the way through to statistically-driven and knowledge-driven interpretations.

Expertise:

We are experienced in developing bioinformatics pipelines, providing data management solutions, analyzing the data using statistical methods and knowledge driven methods, and delivering professional-grade results. We are most familiar with human genomics projects, but have experience with other organisms as well. We are most focused on supporting sequencing projects, but are very capable of supporting array and PCR-based projects as well.

Infrastructure:

We leverage Amazon Web Services for most of our storage (EBS & S3) and computational resources (EC2). We are not frivolous about security, and we can provide you with security documentation to demonstrate how we leverage cloud resources while keeping best-in-class security. We also have powerful 16-core machines in our own private cloud that we leverage for service projects as well.

Years in service: 14

Other services offered by Station X:

Service Description Price
Differential Gene Expression Analysis $1655.00 USD (flat price)
Transcriptome Mapping $100.00 USD (per sample)
Comparative Genome Analysis $2500.00 USD (flat price)
Custom scripting and special projects $275.00 USD (per hour)
Other Services Visualizations, Report Generation, Customizations to our platform, Training, Scientific support, Presentation support, etc. $300.00 USD (per hour)
Read Filtering and Cleaning $115.00 USD (per sample)
Exome Analysis $2500.00 USD (flat price)
Small RNA Mapping $100.00 USD (per sample)
SNP / Indel Mapping $100.00 USD (per sample)
SNP / Indel Calling $100.00 USD (per sample)
SNP/SV/CNV Discovery $100.00 USD (per sample)
Genome Annotation $85.00 USD (per sample)
Small RNA Annotation $85.00 USD (per sample)
Transcriptome Annotation $85.00 USD (per sample)
Variant Annotation $85.00 USD (per sample)

The Africa Genomics Centre and Consultancy (TAGCC) ltd

Kenya

TAGCC is an African company offering services in next generation sequence data analysis and consultancy in genomics. We have implemented a wide range of pipelines to analyse NGS data from various platforms including Illumina and 454. We support design and implementation of genomics and NGS based projects.

Years in service: 10

Other services offered by The Africa Genomics Centre and Consultancy (TAGCC) ltd:

Service Description Price
Differential Gene Expression Analysis We Identify differentially expressed and significant genes from RNA-seq data. Our workflow includes QC clean up, removal of ribosomal RNA contamination followed by denovo or reference based mapping. RPKM/FPKM-based quantitation. $80.00 USD (per sample)
Transcriptome Mapping Map mRNAs to either the reference or the assembled genome. $110.00 USD (per sample)
Other Services Admixture modelling and SNP phylogenetics. Use genetic data to infer the structure and evolutionary history of populations (Time is dependent on VCF/PED file size) $225.00 USD (per hour)
Read Filtering and Cleaning QC analysis, trimming and low quality reads removal. Both Raw and QC trimmed Fastq files will be made available. $24.00 USD (per sample)
Exome Analysis We analyse full exomes from raw sequence data through the process of cleaning, alignment, variant calling to analysis ready vcf file with variants effects summary. $125.00 USD (per sample)
SNP / Indel Mapping Map SNPs and Indels. $110.00 USD (per sample)
Genome Mapping Alignment of NGS data to reference genome and generate mapping statistics $60.00 USD (per sample)
Metagenomic Analysis Generating publication ready Phylogenetic trees, Alpha and beta-diversity, rarefactions, rank abundance plots, relative abundance bar plots, with integration of meta-data, etc. Inquire
SNP / Indel Calling Identify and qualify SNPs and Indels. $110.00 USD (per sample)
Base Calling Demultiplex data and convert BCL or SFF files to FASTQ files. (Time is dependent on file size) $120.00 USD (per hour)

Strand Life Sciences

India

Strand Life Sciences is a technology innovation company that has pioneered the practice of scientific intelligence in health sciences. Strand was established in 2000, with a founding theme “Algorithms for Life”. The company is an academic-spin of in India, founded by four Computer Scientists - Dr. Vijay Chandru, Dr. Ramesh Hariharan, Dr.V. Vinay, and Dr. Swamy Manohar. Since then, we have established a strong portfolio of products for biological systems research and for diagnosis and treatment of diseases. Over 2000 scientific laboratories and 100 hospitals across the world are our clients. Now, we have entered a new era guiding medical decisions using molecular insights with a new theme ‘New Generation Healthcare’.

Strand NGS-Formerly Avadis® NGS is Strand’s flagship product for analysis, management and visualization of next-generation sequencing data. It supports extensive workflows for alignment, RNA-Seq, small RNA-Seq, DNA-Seq, ChIP-Seq, MeDIP-Seq and Methyl-Seq experiments. We provide bioinformatics services using Strand NGS and price is dependent on man hours, number of samples and other factors. Please consult us for more details sales@strandngs.com

Years in service: 14

Other services offered by Strand Life Sciences:

Service Description Price
Differential Gene Expression Analysis $500.00 USD (per sample)
Exome Analysis $500.00 USD (per sample)
ChIP-Seq Analysis Inquire $500.00 USD (per sample)
SNP / Indel Mapping $500.00 USD (per sample)
SNP / Indel Calling $500.00 USD (per sample)
SNP/SV/CNV Discovery $500.00 USD (per sample)
Methylation Analysis $500.00 USD (per sample)

Oklahoma Medical Research Foundation NGS Core

NGS provider United States of America

The OMRF Genomics facility is a universally accessible resource able to provide investigators with massive amounts of sequencing, genotyping, or gene expression data in a relatively short period of time. Our NovaSeq X Plus, NovaSeq 6000, and NextSeq 2000 instruments combine to provide researchers extreme flexibility in a very cost-efficient manner.

Years in service: 15

Other services offered by Oklahoma Medical Research Foundation NGS Core:

Service Description Price
Read Filtering and Cleaning Read trimming of sequencing results $50.00 USD (flat price)
Read Filtering and Cleaning Adapter and base quality trimming to specified level using Trimmomatic. Both Raw and trimmed Fastq will be made available. $50.00 USD (flat price)
Exome Analysis Full exome analysis from raw data to vcf file. Includes read trimming, alignment to reference with BWA, and variant calling utilizing the most up to date GATK pipeline. Deliverable will be a clean, filtered, analysis ready vcf file. Raw data will also be returned. $150.00 USD (per sample)
Genome Mapping Alignment of NGS data to reference genome using BWA. $25.00 USD (per sample)

Center For Cancer Computational Biology

NGS provider United States of America

CCCB has strong experiences in perform and analyze extracellular sRNASeq in addition to the standard mRNASeq, sRNASeq, and ExomeSeq. CCCB also offers comprehensive analytical consulting, project planning, and genomic data visualization tools such as WebMeV (http://mev.tm4.org) to allow researchers with no informatics backing to receive fully analyzed NGS data.

Years in service: 16

Other services offered by Center For Cancer Computational Biology:

Service Description Price
Exome Analysis Turnaround time is estimated after data QC. Expecting fastq files and deliver annotated VCF files. $189.00 USD (per sample)

MedGenome, Inc.

NGS provider United States of America

MedGenome has a next generation sequencing lab based in South San Francisco housing Illumina's NovaSeq, HiSeq X, HiSeq 2500 & MiSeq machines. We specialize in end to end Genomic Services including: DNA/RNA extraction, library prep, sequencing, standard analysis, and advanced analysis.

We offer whole genome, whole exome, RNA sequencing (including low input options), TCR seq (alpha/beta, gamma/delta, FFPE), BCR and single cell sequencing services. We also help labs sequence their pre-made libraries. We offer proprietary tumor microenvironment analysis and neo-epitope prediction as part of our advanced bioinformatics services.

Years in service: 11

Other services offered by MedGenome, Inc.:

Service Description Price
Differential Gene Expression Analysis We offer RNA analysis services. You can provide us FASTQ files we will will provide gene expression, differential expression, pathway analysis reporting $100.00 USD (per sample)
Exome Analysis Alignment and variant calling (BAM and VCF files) Optional somatic mutation analysis and annotation $100.00 USD (per sample)

Labindia-GPOD

India

We provide NGS data analysis services using public domain tools as well as CLC bio workbenches. Our services include primary, secondary and tertiary data analysis of NGs data from all platforms. Data analysis steps include read QC check, Assembly and metrics, Annotation, Variant detection, and annotation and biological interpretations. We also enter in to joint projects as industry partners.

Years in service: 15

Other services offered by Labindia-GPOD:

Service Description Price
Exome Analysis Exome analysis at our facility is performed using CLC bio Cancer workbench which helps in find and annotate variants more accurately. $200.00 USD (per sample)
Genome Mapping We perform reference genome mapping using CLC bio Genomic recent version and also available public domain tools to benchmark the results. CLc bio has currently released faster genome mapper. We perform post assembly metrics to check correctness of reference assembly. $150.00 USD (per sample)
Genome Annotation We perform Genome annotation using BLAST and BLAST2Go tools. We have FPGA based local facility which speeds up the BLAST process $500.00 USD (per sample)
Transcriptome de novo Assembly Transcriptome de novo assembly and read map back is performed using CLC bio genomic workbench and other public domain tools. This analysis is followed by transcriptome annotation and tertiary analysis like pathaway findings. $500.00 USD (per sample)
Variant Annotation Variant annotation is performed using CLC bio Cancer Research Workbench. $600.00 USD (per sample)
Whole Genome de novo Assembly WGS de novo assembly is performed using latest version of the CLC bio Genomic Workbench and available public domain tools. End analysis helps to benchmark the results and robustness of the assembly. Post assembly metrics are performed to check the quality of the assembly $500.00 USD (per sample)

NXT-Dx

NGS provider Belgium

At NXT-Dx we can offer SE50, PE50 and PE100 sequencing on the Illumina HiSeq. On top of this we can also offer different sequencing settings on the Illumina MiSeq and shortly we will also be able to offer sequencing on the Illumina NextSeq.

We can offer sequencing of already prepared libraries but we can also offer full-scope projects whereby we receive cells, tissue, gDNA or RNA and take care of the sample preparation, library prep, sequencing and bio-informatics analysis.

We have worked with samples from all kind of species (mammalian, plant, bacterial) and all kind of cell types.

We pride ourselves in having close contact with our customers and only one single contact point. Also after the delivery of the data, we remain available to answer any questions customers might have on their data, their analysis, etc.

Years in service: 13

Other services offered by NXT-Dx:

Service Description Price
Differential Gene Expression Analysis $170.00 USD (per hour)
Transcriptome Mapping $170.00 USD (per hour)
Comparative Genome Analysis $170.00 USD (per hour)
Custom scripting and special projects $170.00 USD (per hour)
Read Filtering and Cleaning $170.00 USD (per hour)
Exome Analysis $170.00 USD (per hour)
ChIP-Seq Analysis $170.00 USD (per hour)
Small RNA Mapping $170.00 USD (per hour)
Genome Mapping $170.00 USD (per hour)
Targeted Capture Analysis $170.00 USD (per hour)
Genome Annotation $170.00 USD (per hour)
Small RNA Annotation $170.00 USD (per hour)
Methylation Analysis $170.00 USD (per hour)
Transcriptome Annotation $170.00 USD (per hour)
Variant Annotation $170.00 USD (per hour)
Base Calling $170.00 USD (per hour)

Beckman Coulter Genomics

NGS provider United States of America

Beckman Coulter Genomics offers next generation sequencing services designed to meet the evolving sequencing needs of academic, biotechnology and pharmaceutical researchers worldwide. A comprehensive range of next generation sequencing services is available utilizing platforms from Illumina and Roche.

End to end solutions are offered allowing tailoring of projects to your specific needs. A wide variety of bioinformatics packages are available and results consultation is provided to ensure you understand the data returned to you. For the quickest service we accept pre-made libraries for sequencing only projects.

• Expert scientists consult on project design to ensure appropriate experimental approach • Beckman Coulter instrumentation utilized for fully automated library construction and target enrichment with enhanced reproducibility and reliability • Bioinformatics scientists oversee all data analysis to ensure quality
• Videoconference provided for report review and results discussion

Trusted Partner • Over 20 years sequencing experience • 1,500+ customer publications • 200+ successful audits • Experienced staff from well-known institutes of academic and commercial excellence • Contributed sequencing data to • >10 genome projects including mouse, cat, dog and salmon • >100 Microbial and Fungal genomes

Years in service: 19

Other services offered by Beckman Coulter Genomics:

Service Description Price
Differential Gene Expression Analysis $150.00 USD (per sample)
Read Filtering and Cleaning Inquire
Exome Analysis $250.00 USD (per sample)
Metagenomic Analysis Assembly including demultiplexing and standard run report Inquire
SNP / Indel Calling $250.00 USD (per sample)
Targeted Capture Analysis $250.00 USD (per sample)
Small RNA Annotation $150.00 USD (per sample)
Variant Annotation $250.00 USD (per sample)

SciBerg

Germany

We offer computational analyses of Next-Generation Sequencing data (Illumina and Ion Torrent platforms), including RNA-seq, small RNA-seq, DNA-seq, Bisulfite-seq and ChIP-seq. Our bioinformatics support can be fully customized for your research needs, the scope and objectives of the study. We apply only up-to-data well-proven software and pipelines working under Unix/Linux environment. Optionally, our experts can help to interpret the obtained results from the scientific point of view, provided some of them are working in a close research field.

Other services offered by SciBerg:

Service Description Price

HybridStat Predictive Analytics

Greece

HybridStat is a company bringing together a team of highly qualified and motivated scientists and developers, whose expertise spans a variety of statistics and computer science domains. Main HybridStat’s services are centered on bioinformatics, biostatistics and analytics of high-throughput data derived from modern biological technologies such as Next Generation Sequencing (NGS), DNA microarrays and Mass Spectrometry. In addition, HybridStat offers customized software solutions regarding the above.

Regarding NGS, HybridStat offers a variety of one-stop shop data analysis and analytics services, spanning from genome alignments and preprocessing of raw short read fragments, up to analytical and specialized reports and figures describing the results of various NGS protocols including RNA-Seq (quality control, differential expression and splicing analysis, biochemical pathway enrichments etc.), ChIP-Seq (data normalization and peak calling, gene-binding site associations, methylation profiles, motif finding etc.), Whole Exome and Whole Genome Sequencing (data preprocessing, variant calling, filtering, annotation and interpretation, etc.) and Single Cell Sequencing data analysis, using both open source and optimized proprietary pipelines.

HybridStat, can also offer complete support to your organization through its advanced Whole Exome Sequencing analytics platform Clingon (www.clingon-mds.com). Clingon is a complete, integrated one-stop clinical genomics and medical decision support platform which performs data analysis from raw data up to the generation of clinical reports. It uniquely integrates and curates a handful of resources regarding gene-disease and gene product-drug associations as well as curated variant annotation data towards more timely and accurate results and the optimal design of personalized treatment plans.

Years in service: 10

Other services offered by HybridStat Predictive Analytics:

Service Description Price
Differential Gene Expression Analysis A fully descriptive and interactive report is provided. $300.00 USD (flat price)
Comparative Genome Analysis $60.00 USD (per hour)
Custom scripting and special projects $70.00 USD (per hour)
Other Services $70.00 USD (per hour)
Read Filtering and Cleaning $25.00 USD (per sample)
Read Filtering and Cleaning $30.00 USD (per sample)
Read Filtering and Cleaning $20.00 USD (per sample)
Exome Analysis Exome analysis includes quality control, alignment to the reference genome, alignment statistics, variant calling, variant annotation with our proprietary annotation pipeline which guarantees better results especially in indels and gene-disease association reports. $150.00 USD (per sample)
Exome Analysis Exome analysis includes quality control, alignment to the reference genome, alignment statistics, variant calling, variant annotation with our proprietary annotation pipeline which guarantees better results especially in indels and gene-disease association reports. $170.00 USD (per sample)
Exome Analysis Exome analysis includes quality control, alignment to the reference genome, alignment statistics, variant calling, variant annotation with our proprietary annotation pipeline which guarantees better results especially in indels and gene-disease association reports. $200.00 USD (per sample)
ChIP-Seq Analysis ChIP-Seq analysis includes alignment to the reference genome, quality control, enriched region (peak) calling and association of enriched regions with nearby genes. $70.00 USD (per sample)
ChIP-Seq Analysis ChIP-Seq analysis includes alignment to the reference genome, quality control, enriched region (peak) calling and association of enriched regions with nearby genes. $85.00 USD (per sample)
ChIP-Seq Analysis ChIP-Seq analysis includes alignment to the reference genome, quality control, enriched region (peak) calling and association of enriched regions with nearby genes. $100.00 USD (per sample)
SNP / Indel Mapping $30.00 USD (per sample)
SNP / Indel Mapping $25.00 USD (per sample)
SNP / Indel Mapping $40.00 USD (per sample)
Genome Mapping $25.00 USD (per sample)
Genome Mapping $20.00 USD (per sample)
Genome Mapping $30.00 USD (per sample)
SNP / Indel Calling $40.00 USD (per sample)
SNP / Indel Calling $45.00 USD (per sample)
SNP / Indel Calling $50.00 USD (per sample)
Variant Annotation Variant annotation is performed with our proprietary annotation pipeline which guarantees better results especially in indels. $40.00 USD (per sample)
Variant Annotation Variant annotation is performed with our proprietary annotation pipeline which guarantees better results especially in indels. $50.00 USD (per sample)
Variant Annotation Variant annotation is performed with our proprietary annotation pipeline which guarantees better results especially in indels. $60.00 USD (per sample)
Whole Genome de novo Assembly $1000.00 USD (flat price)

iBinom

United States of America

iBinom is a cloud-based NGS data analysis service designed for clinical inherited disease diagnostics needs. We deliver ultrafast, accurate and easy-to-use genome analysis service for medical professionals around the world. Built-in raw data pre-processing ensures a high confidence output. Proprietary machine learning algorithms and sophisticated filtration system leads to ultimately precise interpretation results and reports a short-list of actionable variants. We support all popular data formats: fastq, fastq.gz, bam, vcf, vcf.gz We are platform-independent: Roche Junior, Roche 454, Illumina, Life Technologies

Years in service: 11

Other services offered by iBinom :

Service Description Price
Exome Analysis We offer exome analysis from raw data processing to variant reporting. Our pipeline implements thorough quality control and finely tuned algorithms tuned to achieve the highest precision, sensitivity and specificity of analysis. Our QC system forewarns of potentially missed reporting variants in uncovered regions. We guarantee reproducible and ultimately accurate results. $400.00 USD (per sample)
Genome Annotation We provide an intuitive and flexible genome data filtration system that shortens the path to detecting the causative variants for inherited disease diagnostics. All relevant databases, scores and essential knowledge are plugged into the system. We automatically updates key data points on a regular basis. Free data re-analysis is available. We offer target panel, exome and whole genome variant a… $50.00 USD (per sample)

Omega Bioservices

NGS provider United States of America

Our facility is unique because we offer the full range of NGS service from sample extraction through to data analysis. Sample extraction capabilities and expertise cover the entire spectrum of both environmental and clinical sample types.

Years in service: 12

Other services offered by Omega Bioservices:

Service Description Price
Differential Gene Expression Analysis Identify differentially expressed genes among samples using RNA-seq technique. Human, mouse, rat, fruit fly, cattle, pig, chicken, zebrafish, C. elegans, maize, thale cress, Japonica rice (Oryza sativa) and yeast, up to 7.5gb/sample. $56.00 USD (per sample)
Differential Gene Expression Analysis Custom bioinformatics for non-model organisms, or other unusual cases. Does not include setup fee. $110.00 USD (per sample)
Transcriptome Mapping Map mRNAs to either the reference or the assembled genome. $332.00 USD (per sample)
Custom scripting and special projects We provide study specific bioinformatics analysis (known as tertiary analysis). such as (not limited to) 1) process secondary sequencing data analysis for a variety of platforms such as Nanostring, Nanopore, single cell expression. 2) integrative analysis across sequencing platforms (such as DNA-seq, RNA-seq, Chip-seq) 3) integrate meta/clinical information, perform association study and build p… $60.00 USD (per hour)
Read Filtering and Cleaning Examination of sequencing quality and removal of low quality reads prior to downstream analysis provided free of charge with sequencing service if desired. $110.00 USD (per sample)
Exome Analysis Whole exome sequencing involves capturing the coding region of the genome, or exons (EXpressed regiONS). SNVs and indels are the most important and abundant types of variation in exons. Human exome analysis provided free of charge with sequencing service. $332.00 USD (per sample)
ChIP-Seq Analysis ChIP-Seq is a technique to identify DNA loci bound by a specific protein. The standard output of ChIP-seq analysis includes peak call and motif enrichment at binidng sites. $332.00 USD (per sample)
Small RNA Mapping Small RNA (miRNA, lincRNA, snoRNA, snRNA, tRNA) libraries will be mapped to the reference genome and annotated using public databases e.g. miRBase. $221.00 USD (per sample)
SNP / Indel Mapping Mapped to the reference genome and annotated using public database. Analysis for human, mouse, and rat provided free of charge with sequencing service. $332.00 USD (per sample)
Genome Mapping Genome mapping is a technique used to assign the location of a particular gene on a chromosome and measure their relative locations and distances between genes. Mapping to many model organisms provided free of charge with sequencing service. $110.00 USD (per sample)
Metagenomic Analysis Metagenomic analysis involves the identification and quantification of genetic material from environmental, uncultured microorganisms. Analysis involving only 16S rRNA amplicon sequences are provided free of charge with sequencing service. $551.00 USD (per sample)
SNP / Indel Calling Identify SNPs and Indels in the region of interested, using DNA sequencing. Analysis for human, mouse, and rat provided free of charge with sequencing service. $332.00 USD (per sample)
SNP/SV/CNV Discovery Variants discovery. Analysis for human, mouse, and rat provided free of charge with sequencing service. $332.00 USD (per sample)
Targeted Capture Analysis Variant call, gene annotation. Provided free of charge with sequencing service. $332.00 USD (per sample)
Genome Annotation Annotation is the process by which pertinent information about these raw DNA sequences is added to the genome databases. This involves describing different regions of the sequence and identifying which regions can be called genes. $221.00 USD (per sample)
Small RNA Annotation Small RNA (miRNA, lincRNA, snoRNA, snRNA, tRNA) libraries will be mapped to the reference genome and annotated using public databases e.g. miRBase. $332.00 USD (per sample)
Methylation Analysis The processing of bisulfite sequencing data includes sequence alignment and the quantification of absolute DNA methylation at base resolution. Methylation analysis for data generated from the Illumina TruSeq kit are provided free of charge with sequencing service. $553.00 USD (per sample)
Transcriptome de novo Assembly Identify and quantify putative mRNA transcripts using RNA-seq data for unannotated species. $553.00 USD (per sample)
Transcriptome Annotation Annotate or predict functions of transcribed genes using well know gene ontology tools. $332.00 USD (per sample)
Variant Annotation Identified variants will be mapped to the reference genome and annotated using public database. Analysis for human sequences provided free of charge with sequencing service. $332.00 USD (per sample)
Whole Genome de novo Assembly Prices vary according to genome type. Please contact our Science Project Team. Some small genome assembly provided free of charge with sequencing service. $3315.00 USD (per sample)
Base Calling Demultiplex data and convert BCL files to FASTQ files $110.00 USD (per sample)

Applied Biological Materials Inc.

NGS provider Canada

Committed to making newer technologies attainable to modern researchers, abm offers a wide range of sequencing services on the advanced Illumina® sequencing platforms at accessible prices and rapid turnaround times. abm's premium NGS services will not only save valuable time and money, but also provide the most reliable and comprehensive solution for the project's needs.

Advantages of using our NGS services: -dedicated NGS specialists to help with experimental design and data analysis -customizable bioinformatics analysis to suit your project needs -strict quality control at multiple steps in library preparation and sequencing -RNA-seq, miRNA-seq, WGS, metagenomics, Amplicon-Seq and more!

What types of bioinformatics analysis will be done? If the reference genome is available (i.e. human or mouse), read mapping and alignment to the reference genome is included in the service. -Data is available in industry standard formats: FASTQ (default), SFF or BAM. Other formats available upon request (additional fees may apply). -RNA-seq includes: Read mapping and gene expression level estimation

Our data report files are provided in formats that can be viewed with any standard text viewers.

Years in service: 11

Other services offered by Applied Biological Materials Inc.:

Service Description Price

One Health Innovation Lab

NGS provider United States of America

At the forefront of scientific advancement, our sequencing and biorepository facility is part of the One Health Shared Services at Innovation Foundation dedicated to enhancing the health and well-being of humans, animals, and ecosystems.

Our mission: To advance health across boundaries.

Sequencing platforms: NextSeq2000: Versatile Illumina platform for flexibility and speed. MiniSeq: Compact and cost-effective, suitable for targeted sequencing and small-scale applications.

We offer cutting-edge genomic research services & Bioinformatics support. Bioinformatics Support: Our bioinformatics experts collaborate closely with you.

Why Choose Us? Accuracy: Our cutting-edge technology ensures reliable results. Fast Turnaround: Get your data quickly without compromising quality. Expert Support: Our scientists are here to assist you. Custom Solutions: Tailored services to meet your specific research goals. End-to-end solutions: From experimental design to data analysis, we guide you every step of the way.

Contact Us at OHIL@okstate.edu to discuss your sequencing needs or possible collaborations with the One Health Innovation Lab.

Other services offered by One Health Innovation Lab:

Service Description Price
Differential Gene Expression Analysis Differential Gene Expression Analysis from RNAseq data. Input - gene counts from RNAseq (output from Transcriptome Mapping) Deliverables - PCA plot showing sample clustering, MA plot (log2 fold changes in gene expression between groups with significant calls highlighted), list of Differentially Expressed Genes (DEGs), GSEA or GO Analysis on DEGs Note: Price advertised is per biological compar… $50.00 USD (per sample)
Transcriptome Mapping Alignment of RNAseq data to the reference genome, removal of PCR duplicates, report of alignment statistics with gene counts. Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats, gene counts $50.00 USD (per sample)
Custom scripting and special projects Custom scripting or analysis, data visualization assistance, and additional services are available starting around $20 per sample. Please reach out to us to get a more accurate quote - we'd love to help you with your project! $20.00 USD (per sample)
Exome Analysis Analysis of targeted exome sequencing. Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats, exome panel coverage stats $50.00 USD (per sample)
Genome Mapping FOR WHOLE GENOME SEQUENCING ALIGNMENT ONLY. Includes alignment of .fastq file to reference genome, removal of PCR duplicates, and report of alignment quality. Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats $150.00 USD (per sample)
Genome Mapping FOR TARGETED AMPLICON SEQUENCING ALIGNMENT ONLY. Includes alignment of .fastq file to reference genome, removal of PCR duplicates, and report of alignment quality. Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats $50.00 USD (per sample)
SNP/SV/CNV Discovery Variant calling analysis on aligned genomic data. Input - .bam file (alignment) Deliverables - .vcf file of variants $20.00 USD (per sample)
Targeted Capture Analysis For data types such as ChIPseq, ATACseq, CUT and RUN, etc, in which amplicons are targeted for sequencing. Includes alignment to the reference genome, removal of PCR duplicates, a report of alignment quality, and calling of "peaks"/"binding sites". Input - .fastq file Deliverables - fastqc report, bam file (sorted, PCR duplicates removed), alignment stats, binding site/"peak" calls (w/ and w/o … $50.00 USD (per sample)
Base Calling Base calling from .bcl file. Input - .bcl file Deliverables - fastq file and fastqc report $20.00 USD (per sample)

Bioinformatics Unit, Panacea Biosciences

NGS provider India

Other services offered by Bioinformatics Unit, Panacea Biosciences:

Service Description Price
Read Filtering and Cleaning $40.00 USD (per sample)
Exome Analysis End to End Exome-Seq Data Analysis $75.00 USD (per sample)
ChIP-Seq Analysis we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis. $80.00 USD (per sample)
Genome Mapping Available only for Human, Mouse and available sequenced geneomes $75.00 USD (per sample)
SNP/SV/CNV Discovery End to End variant analysis $70.00 USD (per sample)
Small RNA Annotation Available only for Human, Mouse and available sequenced geneomes $60.00 USD (per sample)
Base Calling Base calling is the process of assigning bases (nucleobases) to chromatogram peaks. One computer program for accomplishing this job is Phred base-calling, which is a widely used basecalling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy. $50.00 USD (per sample)

CD Genomics

NGS provider United States of America

We specialize in the services of DNA sequencing, genotyping, DNA library construction and aptamer development. Shotgun Library Sequencing, cDNA Library Sequencing, SAGE Library Sequencing, Whole Genome Sequencing and Primer Walking Sequencing. we offer high quality Re-sequencing & SNP Discovery Services. Quite a few of our staff scientists once participated in the International HapMap Project too.

extensive experience in whole genome shotgun sequencing services. Beginning from bacterial cells or genomic DNA, we provide you with accurate genome consensus sequences. We are also experienced in genome annotation and comparative genomics research. Notably our staff scientists have finished a number of whole microbial genome sequencing projects, such as the genomes of Pseudomonas bathycetes, Bacillus thuringiensis, Thermoanaerobacter tengcongensis, Streptococcus suis, and quite a few virus genomes. In addition, our in-house Laboratory Information Management System (LIMS) as well as manual basecalling ensures the highest service quality.

CD Genomics has been offering professional DNA library construction services for over 5 years. Hundreds of various cDNA libraries (such as standard cDNA library, large insert cDNA library, normalized cDNA library and subtracted cDNA library) and genomic DNA libraries (including short-insert plasmid shotgun library, large-insert plasmid shotgun library, whole genome shotgun library, Fosmid library, Cosmid library, MiniBAC and BAC library) have been constructed in our lab

CD Genomics has been dedicated to provide a full range of services to develop high quality customized aptamers for research, diagnostic and therapeutic applications. Services offered by CD Genomics include aptamer synthesis, aptamer generation, cell aptamer selection, aptamer design and modification, negative selection and so on.

Years in service: 19

Other services offered by CD Genomics:

Service Description Price
Other Services We provide statistical and bioinformatic data analysis services that help explain the large amounts of data commonly generated by next generation sequencing and genotyping experiments. Our bioinformatic staff consists of all PhD-level scientists trained in bioinformatics, biology and statistics. The software infrastructure for analysis is a combination of custom-built and open-source software. O… Inquire
SNP / Indel Mapping CD genomics can help you analyze genetic variation efficiently to meet diverse research needs. By utilizing Affymetrix and Illumina array platforms, we support high-throughput and multiplex processing to meet diverse research needs, delivering high-quality data at a low per-sample cost. Advantages of SNP Microarray Custom, flexible, and scalable; High call rates (> 99%) and high accuracy; Cost-… $80.00 USD (per sample)
Metagenomic Analysis Key Features and Advantages Longest average read lengths, with~50% of reads longer than 50kb, which exceeds the size of repetitive elements in the average bacterial genome. No DNA amplification. Highest consensus accuracy, low sequencing-context bias Novel bioinformatics analysis programs and pipelines Well-experienced personnel Sample Requirements: gDNA≥5 ug Sequencing Strategy: PacBio Platfo… 120.00

Leucine Rich Bio

India

Leveraging the expanding prospects of microbiome research, Leucine Rich Bion has integrated a robust computational pipeline "MetaRich" into a user-friendlyplatform for comprehensive analyses of any microbiome data.

After rigorous testing & validation of several leading microbiome analysis pipelines, tools & databases, we have compiled “MetaRich” to analyze both 16s rDNA & shotgun metagenomes, duly supplemented by our in-house computational tools. MetaRich will assist both researchers & industry personnel who are in pursuit of discovering biological insights within complex microbial systems & will ease the arduous task of large-scale microbiome data analysis.

Years in service: 10

Other services offered by Leucine Rich Bio:

Service Description Price
Microbiome Analysis For Individual Samples Abundance data - Raw & % Normalized Abundance Bar plots - Raw & % Normalized Pie charts - Kingdom through Phylum Alpha diversity Plots & index value table AMR Prediction Comparative Analyses Differential abundance data (across groups) Abundance Bar plots Raw & % Normalized Alpha diversity Plots & index value table Beta diversity Plots & index value table PCoA analysis & pl… $9.00 USD (per sample)

Amby Lab

NGS provider United States of America

We offer user friendly sequencing services on HiSeq 2500 platform.

We always use only original kits and protocols and our sequencing platforms are maintained and updated promptly, that guarantees the highest quality of the data.

Professionally performed analysis of large scale sequencing data allows making breakthrough investigations, which previously required years of exhausting routine work. With over years of data analyzing experience we have matured team of experts in practical data processing which can find out as much useful information from original sequencing and genotyping data, as possible!

Years in service: 14

Other services offered by Amby Lab:

Service Description Price
Exome Analysis 7 - 9 Gb of reads (i.e. 60 Mb target with 150x mean coverage). Analysis of WES or any other custom panel results in the following VCF output: SNP and INDEL calling. CNV (longer than 5 exons) is available after collection of data for more than 20-30 samples with common enrichement assay. Mapping of variants to 1000Genomes, clinvar, ExAC, hapmap, hgmd etc. With annotation of called variants. $72.00 USD (per sample)
Exome Analysis <3 Gb of reads (i.e. 60 Mb target with 50x mean coverage). Analysis of WES or any other custom panel results in the following VCF output: SNP and INDEL calling. CNV (longer than 5 exons) is available after collection of data for more than 20-30 samples with common enrichement assay. Mapping of variants to 1000Genomes, clinvar, ExAC, hapmap, hgmd etc. With annotation of called variants. $28.00 USD (per sample)
Exome Analysis 4 - 6 Gb of reads (i.e. 60 Mb target with 100x mean coverage). Analysis of WES or any other custom panel results in the following VCF output: SNP and INDEL calling. CNV (longer than 5 exons) is available after collection of data for more than 20-30 samples with common enrichement assay. Mapping of variants to 1000Genomes, clinvar, ExAC, hapmap, hgmd etc. With annotation of called variants. $50.00 USD (per sample)
Exome Analysis 10 - 15 Gb of reads (i.e. 60 Mb target with 200x mean coverage). Analysis of WES or any other custom panel results in the following VCF output: SNP and INDEL calling. CNV (longer than 5 exons) is available after collection of data for more than 20-30 samples with common enrichement assay. Mapping of variants to 1000Genomes, clinvar, ExAC, hapmap, hgmd etc. With annotation of called variants. $94.00 USD (per sample)

Dreamgenics

NGS provider Spain

Dreamgenics is a biotech company that offers bioinformatics analysis services for genomic, transcriptomic and metagenomic NGS data using our Genome One software. Genome One (CE-IVD certified) is an advanced tool that allows the integration of all the bioinformatics solutions required for the study, including read alignment, variant calling and annotation. Our analyses identify high-quality genomic variants through high sensitivity and specificity standards, extracting important biological information and reducing validation costs. The services that we offer are the following: WGS, WES, Gene panels, Transcriptomics (RNA-Seq) and Metagenomics. Additionally, we hand in the results using our web viewer Genome One Reports (https://www.dreamgenics.com/en/genome-one/).

The use of our bioinformatics tools allows us to offer you high-quality results in a fast and simple way. By using our analysis services, you considerably reduce costs and the investment in technological devices, informatics and qualified professionals.

Lastly, we are an ISO 9001:2015, UNE-EN ISO 13485:2018 and UNE-ISO/IEC 27001:2017 certified company which represents our commitment to provide our customers with products and services that meet the most demanding quality standards.

Years in service: 13

Other services offered by Dreamgenics:

Service Description Price
Single Cell RNA-Seq Analysis We offer Single cell RNA-Seq bioinformatic analysis from FASTQ files including: - Sequencing and mapping quality control. - Alignment of reads against reference genome. - Quantification of gene expression at the single cell level. - Reduction of data dimensionality. - Clustering or division of cells into different groups and subgroups. - Differential gene expression analysis. - Study of the evol… $200.00 USD (per sample)
Differential Gene Expression Analysis Our RNA-Seq analysis includes: Quality control, Alignment, Quantification of gene expression, Differential gene expression analysis and Enrichment study of gene ontologies and pathways. It can also include the study of isoforms generated in alternative splicing events and the identification of other RNAs (smallRNAs and ncRNAs)*. We will deliver the results to the Genohub data bucket as well as t… $90.00 USD (per sample)
Exome Analysis Our bioinformatics analysis includes: Quality control, Alignment, Detection of high quality variants (SNVs, translocations and CNVs), Filtering of common variants, Annotation of variants obtained with multiple databases and prediction algorithms and Comparison between samples and extraction of recurrent variants. We will deliver the results to the Genohub data bucket as well as through our platf… $80.00 USD (per sample)
Transcriptome Annotation Our RNA-Seq analysis includes: Quality control, Alignment, Quantification of gene expression, Differential gene expression analysis and Enrichment study of gene ontologies and pathways. It can also include the study of isoforms generated in alternative splicing events and the identification of other RNAs (smallRNAs and ncRNAs)*. We will deliver the results to the Genohub data bucket as well as t… $90.00 USD (per sample)

DNA Link Inc.

NGS provider United States of America

DNA Link was founded in 2000. In the beginning, we offered genome analysis for Universities and Government Institutes supporting a lot of joint research projects. Later we became involved in larger research projects funded by the government and expanded our market to all research, Biotech, Pharmaceutical, foreign institutes and companies. Based on our 20 year-experiences, DNA Link provides options and services in Next generation sequencing, Genotyping, Microarray, Forensics and also personal genomics. Our expertise in research on SNP discovery has lead DNA Link to develop novel personal identification systems called AccuID. DNALink USA, Inc, is based in Los Angeles, CA

Years in service: 24

Other services offered by DNA Link Inc.:

Service Description Price
Transcriptome Mapping 1. Basic bioinformatics analysis  Sequencing Summary  Alignment Summary  Summarizing plots o Density plot, Box plot, GSEA, Scatter plot, Volcano plot  List of genes expressed differentially between given classes  List of transcripts expressed differentially between given classes  Pathway analysis using DAVID 2. Advanced bioinformatics analysis (optional)  Fusion gene analysi… Inquire
Exome Analysis 1. Basic bioinformatics analysis: Analysis using GATK(2.7) best practices guideline  Sequencing Summary Alignment Summary Depth Coverage Plot Genotype Calling and SNP detection Germline & Somatic Variant Summary and Annotation ○ Prediction Amino acid substitution and risk score(SIFT, PolyPhen, Phylop, mutationTaster and so on) ○ Frequency estimation using 1000genome and ESP4500 2.… Inquire
ChIP-Seq Analysis 1. Basic bioinformatics analysis  Sequencing Summary  Alignment Summary  List of peak positions identified by ChIP-seq tools  Input data is transformed into applicable bam or wig format, as needed for visualization by commonly used genome browsers (e.g. IGV or UCSC Genome Browser) 2. Advanced bioinformatics analysis (optional)  Medip  Peak analyzer  Customized Analysis(Client… Inquire
Small RNA Mapping 1. Basic bioinformatics analysis  Sequencing Summary  Alignment Summary  Visualization plot o Density plot, Box plot, GSEA, Scatter plot, Volcano plot 2. Advanced bioinformatics analysis (optional)  Target scan Analysis (limited to specific species)  Pathway Analysis  Customized Analysis(Client Support) Inquire
Genome Mapping 1. Basic bioinformatics analysis  Analysis using GATK(2.7) best practices guideline  Sequencing Summary  Alignment Summary  Depth Coverage Plot  Genotype Calling and SNP detection  Germline & Somatic Variant Summary and Annotation ○ Prediction Amino acid substitution and risk score(SIFT, PolyPhen, Phylop, mutationTaster and so on) ○ Frequency estimation using 1000genome and ESP450… Inquire
Targeted Capture Analysis  Analysis using GATK(2.7) best practices guideline  Sequencing Summary  Alignment Summary  Depth Coverage Plot  Genotype Calling and SNP detection  Variant Summary and Annotation ○ Prediction Amino acid substitution and risk score(SIFT, PolyPhen, Phylop, mutationTaster and so on) ○ Frequency estimation using 1000genome and ESP4500 2. Advanced bioinformatics analysis (optional)… Inquire
Methylation Analysis 1. Basic bioinformatics analysis  Sequencing Summary  Alignment Summary  List of peak positions identified by ChIP-seq tools  Input data is transformed into applicable bam or wig format, as needed for visualization by commonly used genome browsers (e.g. IGV or UCSC Genome Browser) 2. Advanced bioinformatics analysis (optional)  Medip  Peak analyzer  Customized Analysis(Cli… Inquire
Whole Genome de novo Assembly  Sequencing Summary  Pre-Assemble ( Error correction )  De novo Assembly ( contig, scaffold )  Consensus Polishing  Gene prediction ( need RNA-seq data for Eukaryotes )  Genome plot 2. Advanced bioinformatics analysis (optional)  De novo Assembly ( contig, scaffold )  Gene Annotation ( Gene Ontology )  Customized Analysis (Client Support) Inquire

Diploid

Belgium

At Diploid, we turn NGS data into clinical reports or research reports, allowing hospitals, commercial labs and research institutes to outsource human genome interpretation.

Our focus is on 3 major areas: - Rare disease diagnostics - Carrier screening - Cancer

With high-quality diagnostics, fast turn-around times, secure infrastructure, and a personal approach, Diploid is rapidly becoming a trusted partner for genetic departments and commercial labs worldwide.

Over the past few months, we have been working for the following institutes and labs: - Oxford University Hospitals (UK) - University of Verona (Italy) - Otogenetics (US) - Macrogen (US) - King Faisal Specialist Hospital (KSA) - National Reference Lab (UAE)

Years in service: 10

Other services offered by Diploid:

Service Description Price
Custom scripting and special projects Contact us for custom bioinformatics development Inquire
Exome Analysis - Starting from BAM or VCF - Data can be delivered by secure online upload or by HDD shipment - Extensive clinical or research report, signed by a certified clinical geneticist - 14 business days turn around time - Optional Fast-track service (7 days TAT) - First 3 analyses are FREE Inquire

CEN4GEN Institute for Genomics and Molecular Diagnostics

NGS provider Canada

Established in 2014, CEN4GEN® Institute for Genomics and Molecular Diagnostics is a Canadian owned, award winning, licensed private corporation, which excels as a leader in providing diverse services for genomics applications: DNA testing / Genetic testing / Precision Medicine / Personalized Medicine / Preventive Medicine / Genome Medicine. Our distinguished team comprises of highly qualified clinicians, medical scientists, scientists, customer support personnel, product manufacturing and quality control personnel who are experienced in the services and products that we provide. CEN4GEN is proud to provide its cutting edge services so far to clients in Canada, as well as overseas countries in North America, Central America, South America, the Caribbean, Africa, Asia, Europe and the Oceania (specifically Australia and New Zealand). Our clients are from hospitals, universities, clinics, government agencies, commercial entities and private individuals.

CEN4GEN® is committed to providing you with outstanding quality, vital, cost-effective, comprehensive and cutting-edge services using leading-edge technologies.

Years in service: 10

Other services offered by CEN4GEN Institute for Genomics and Molecular Diagnostics:

Service Description Price
Exome Analysis Established in 2014, we are a Canadian owned, award winning, licensed private corporation, which excels as a leader in providing diverse services for genomics applications. We support clients by offering innovative, high quality, efficient and cost effective clinical grade bioinformatics data analysis services. We have so far supported clients from five continents who undertook our services. … $75.00 USD (per sample)
SNP / Indel Calling Established in 2014, we are a Canadian owned, award winning, licensed private corporation, which excels as a leader in providing diverse services for genomics applications. We support clients by offering innovative, high quality, efficient and cost effective clinical grade bioinformatics data analysis services. We have so far supported clients from five continents who undertook our services. … $100.00 USD (per sample)