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 31)


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: 6

Other services offered by Geno-plex Bioinformatics Services:

Service Description Price
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)
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)
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
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)
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)
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)

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: 8

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: 4

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/SV/CNV Discovery Complete CNV processing from sequencing data to final report using know CNV baseline $30.00 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)
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 located in Pasadena, CA. with a focus on developing new technologies to allow scientists/physicians to obtain more results in less time. We provide NGS service as well as related reagents to investigate the functions of identified variants. We also help physicians to unleash the power of NGS in disease diagnosis.

★We have one HiSeq 4000, two NextSeq500, one MiSeq and one Ion Proton. We have --Fast turn around time (our HiSeq4000 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 purpose

★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 screening 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: 6

Other services offered by Quick Biology Inc.:

Service Description Price
Differential Gene Expression Analysis $170.00 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 $170.00 USD (per sample)

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/partnerships/

Years in service: 7

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 http://www.admerahttps://www.admerahealth.com/genomics-and-bioinformatics/ $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 http://www.admerahttps://www.admerahealth.com/genomics-and-bioinformatics/ $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 http://www.admerahttps://www.admerahealth.com/genomics-and-bioinformatics/ $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: 10

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)
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)
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)
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)
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. $100.00 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: 5

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)

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
SNP / Indel Calling Inquire
Read Filtering and Cleaning Inquire
Base Calling Inquire
Targeted Capture Analysis Inquire
Differential Gene Expression Analysis Inquire
Genome Mapping Inquire
Small RNA Mapping Inquire
Exome Analysis Inquire
Transcriptome Mapping Inquire
Genome Annotation Inquire
Transcriptome Annotation Inquire
Custom scripting and special projects Inquire
Transcriptome de novo Assembly Inquire
Other Services Inquire
SNP / Indel Mapping Inquire
Small RNA Annotation Inquire
SNP/SV/CNV Discovery Inquire
Methylation Analysis Inquire
ChIP-Seq Analysis Inquire
Variant Annotation 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
SNP / Indel Calling Inquire
Read Filtering and Cleaning Inquire
ChIP-Seq Analysis Inquire
Genome Mapping Inquire
Variant Annotation Inquire
Small RNA Mapping Inquire
Transcriptome Mapping Inquire
Small RNA Annotation Inquire
Methylation Analysis Inquire
Custom scripting and special projects Inquire
SNP / Indel Mapping Inquire
Transcriptome Annotation Inquire
Differential Gene Expression Analysis Inquire
Exome Analysis Inquire
SNP/SV/CNV Discovery 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: 10

Other services offered by ContigExpress, LLC:

Service Description Price
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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

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: 9

Other services offered by Station X:

Service Description Price
Exome Analysis $2500.00 USD (flat price)
Differential Gene Expression Analysis $1655.00 USD (flat price)
Small RNA Annotation $85.00 USD (per sample)
Small RNA Mapping $100.00 USD (per sample)
SNP / Indel Calling $100.00 USD (per sample)
SNP / Indel Mapping $100.00 USD (per sample)
Transcriptome Annotation $85.00 USD (per sample)
Variant Annotation $85.00 USD (per sample)
Custom scripting and special projects $275.00 USD (per hour)
Comparative Genome Analysis $2500.00 USD (flat price)
SNP/SV/CNV Discovery $100.00 USD (per sample)
Read Filtering and Cleaning $115.00 USD (per sample)
Other Services Visualizations, Report Generation, Customizations to our platform, Training, Scientific support, Presentation support, etc. $300.00 USD (per hour)
Genome Annotation $85.00 USD (per sample)
Transcriptome Mapping $100.00 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: 5

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

Service Description Price
Base Calling Demultiplex data and convert BCL or SFF files to FASTQ files. (Time is dependent on file size) $120.00 USD (per hour)
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)
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
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)
SNP / Indel Calling Identify and qualify SNPs and Indels. $110.00 USD (per sample)
SNP / Indel Mapping Map SNPs and Indels. $110.00 USD (per sample)
Transcriptome Mapping Map mRNAs to either the reference or the assembled genome. $110.00 USD (per sample)
Genome Mapping Alignment of NGS data to reference genome and generate mapping statistics $60.00 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)
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)

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: 9

Other services offered by Strand Life Sciences:

Service Description Price
ChIP-Seq Analysis Inquire $500.00 USD (per sample)
Differential Gene Expression Analysis $500.00 USD (per sample)
Exome Analysis $500.00 USD (per sample)
Methylation Analysis $500.00 USD (per sample)
SNP/SV/CNV Discovery $500.00 USD (per sample)
SNP / Indel Calling $500.00 USD (per sample)
SNP / Indel Mapping $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 Hiseq 3000, NextSeq 500, and Miseq instruments combine to provide researchers extreme flexibility in a very cost-efficient manner.

The facility is capable of processing and analyzing all forms of sequencing projects, including whole genome sequencing, custom targeted resequencing including exome capture, RNA-seq, ChIP-seq, and MethylCap-Seq. Study sample sizes can range from singletons to hundreds or even a thousand samples.

As an Agilent Certified Service Provider we specialize in human exome resequencing and have completed over 2000 human exome sequences to date.

Years in service: 10

Other services offered by Oklahoma Medical Research Foundation NGS Core:

Service Description Price

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: 11

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: 6

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: 10

Other services offered by Labindia-GPOD:

Service Description Price
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)
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 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)
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)
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)

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: 8

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: 14

Other services offered by Beckman Coulter Genomics:

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

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
Differential Gene Expression Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
Transcriptome Mapping Inquire
Custom scripting and special projects Inquire
Other Services Inquire
Exome Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
ChIP-Seq Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
Small RNA Mapping Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
SNP/SV/CNV Discovery Inquire
Genome Annotation Inquire
Small RNA Annotation Inquire
Methylation Analysis € 1.32 per 1 million reads + € 13.20 commission per each sample Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire

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: 5

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 $20.00 USD (per sample)
Read Filtering and Cleaning $25.00 USD (per sample)
Read Filtering and Cleaning $30.00 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)
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)
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. $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. $100.00 USD (per sample)
SNP / Indel Mapping $40.00 USD (per sample)
SNP / Indel Mapping $25.00 USD (per sample)
SNP / Indel Mapping $30.00 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 $50.00 USD (per sample)
SNP / Indel Calling $45.00 USD (per sample)
SNP / Indel Calling $40.00 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)
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. $40.00 USD (per sample)
Whole Genome de novo Assembly $1000.00 USD (flat price)

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: 7

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 are open to your custom analysis projects. Set up a call with our Project Scientist team today to discuss your needs and obtain a quote. $500.00 USD (per sample)
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: 6

Other services offered by Applied Biological Materials Inc.:

Service Description Price
Differential Gene Expression Analysis Service includes: 1) Principal component analysis; 2) Differential gene expression analysis; 3) Gene expression clustering; 4) Full analysis report $222.00 USD (per sample)
Exome Analysis Service includes: 1) Read mapping; 2) deduplication, local realignment and base recalibration; 3) Variation calling; 4) Variation annotation (dbSNP, COSMIC, ClinVar, 1000 Genome); 5) Full analysis report $95.00 USD (per sample)
Metagenomic Analysis Service includes: 1) Contig assembly; 2) OTU clustering and classification; 3) Alpha/beta diversity analysis; 4) Full analysis report; $35.00 USD (per sample)
SNP / Indel Calling Service available for WGS and WES to include: 1) Read mapping; 2) De-duplication, base quality recalibration, and local realignment; 3) SNP and Indel calling $225.00 USD (per sample)
Genome Annotation Service includes: 1) Gene prediction; 2) Functional annotation from KEGG, GO, NCBI $333.00 USD (per sample)
Whole Genome de novo Assembly Service for De novo assembly of genome size < 10Mb. $350.00 USD (per sample)
Microbiome Analysis Service includes: 1) Contig assembly; 2) OTU clustering and classification; 3) Alpha/beta diversity analysis; 4) Full analysis report; $35.00 USD (per sample)

Bioinformatics Unit, Panacea Biosciences

NGS provider India

Other services offered by Bioinformatics Unit, Panacea Biosciences:

Service Description Price
Custom scripting and special projects Based on project requirements. $15.00 USD (per hour)
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)

Leucine Rich Bio

India

Other services offered by Leucine Rich Bio:

Service Description Price
Read Filtering and Cleaning Leucine Rich Bio offers Read filtering, cleaning and quality control analysis. We also offer statistical and heuristic analysis. Literature mining services are also provided. As we are Bangalore (India) based company, we offer very competitive pricing. $75.00 USD (per sample)
Transcriptome Annotation Inquire
Small RNA Annotation Inquire
Transcriptome Mapping Inquire
Comparative Genome Analysis Inquire
Variant Annotation Inquire
Differential Gene Expression Analysis Inquire
Targeted Capture Analysis Inquire
SNP / Indel Calling Inquire
SNP / Indel Mapping Inquire
Transcriptome de novo Assembly Inquire
Exome Analysis Inquire
Whole Genome de novo Assembly Inquire
SNP/SV/CNV Discovery Inquire
Custom scripting and special projects Inquire
Genome Annotation Inquire
Genome Mapping Inquire
ChIP-Seq Analysis Inquire
Metagenomic Analysis Inquire
Microbiome Analysis Inquire

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: 9

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 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)
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 <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)

DREAMgenics

NGS provider Spain

We offer bioinformatics analysis services for human and other organisms genomic and transcriptomic NGS data.

  • Our team of experts offers a completely personalized consulting service, including scientific and technical solutions to your needs. We help you to obtain the best results from your analysis.

  • Our collaboration with the most reliable sequencing providers allow us to select the most suitable platform for your project. We also can assist you in all steps prior to sequencing, such us sample and library preparation and quality controls.

  • DREAMgenics bioinformatics framework has been designed to readily adapt to your needs. Capable of integrating your own algorithms, pipelines and databases to complement the data analysis and interpretation.

  • Our analyses identify high quality genomic variants through excellent sensitivity and specificity standards, extracting meaningful biological information and reducing validation process costs. The results will be delivered through a detailed report.

  • We offer the possibility of advanced visualization and interactive review of results through our exclusive DG Reports web application. (Filtering and priorization of variants, Pre-classification of variants, Graphic interface (genomic browser), Statistics and quality controls, Exportable information, Automated generation of reports).

All our procedures meet with the requirements set by the new General Data Protection Regulation.

Years in service: 8

Other services offered by DREAMgenics:

Service Description Price
ChIP-Seq Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Exome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Base Calling https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Comparative Genome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Custom scripting and special projects https://www.dreamgenics.com/en/bioinformatics-services/ https://www.dreamgenics.com/en/research-projects/ Inquire
Other Services - Research projects https://www.dreamgenics.com/en/research-projects/ - Bioinformatics software design and developments https://www.dreamgenics.com/en/hd-genome-one-en/ - Gene and/or regions of interest panels, ATAC Seq, Family studies, trio analysis.. https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Differential Gene Expression Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Genome Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Genome Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Metagenomic Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Methylation Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Microbiome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Read Filtering and Cleaning https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Small RNA Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Small RNA Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP / Indel Calling https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP / Indel Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP/SV/CNV Discovery https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Targeted Capture Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome de novo Assembly https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Variant Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Whole Genome de novo Assembly https://www.dreamgenics.com/en/bioinformatics-services/ 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: 5

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 - See http://www.diploid.com/service for more info Inquire

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: 6

Other services offered by iBinom :

Service Description Price
Exome Analysis We offer exome analysis from raw data processing to variant reporting. The iBinom 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 iBinom provides 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. iBinom automatically updates key data points on a regular basis. Free data re-analysis is available. We offer target panel, exome and whole genom… $50.00 USD (per sample)