Variant Annotation


Variant annotation tools function by not only providing variant calls but auxiliary data to those variants. These elements of annotation typically include:

1) A definition of the variant, measure of likelihood, genotype

2) Identification of the gene that overlaps with the variant

3) Determination of whether the variant is in an exon

4) Determination of whether it is in a coding region

5) If a SNV, a determination of whether the encoded amino acid is misense

6) Location determination - is it before or after a exon/intron boundary

7) If the variant adds or deletes nucleotides it is annotated as an insertion or deletion.

Providers offering Variant Annotation (found 31)


Kovid BioAnalytics

India

Kovid BioAnalytics is an Informatics and Analytics company based in India. We specialize in building software, web-based or standalone applications for various bioinformatics projects, data curation and analysis services, etc. With a team of Bioinformatics experts and Software Developers we provide the following services: 1) Bioinformatics Software Development 2) Website Design and Maintenance for Bioinformatics Services 3) Curation of Genomics/Proteomics Data 4) Manual annotation of bioinformatics data and data mining 5) Technical writing services 6) Significance Analysis of micro-array data

Years in service: 6

Other services offered by Kovid BioAnalytics:

Service Description Price
Differential Gene Expression Analysis We have experience in performing Differential Gene Expression Analysis for various researchers from institutes like Washington University at St. Louis, West Mead Hospital (Australia), Spain Cancer Center and Bar Ilan University (Israel), etc. $16.57 USD (per hour)
Other Services We have a team of 5 experienced Bioinformatics Experts and 2 web developers, that can built custom pipelines for NGS data analysis, web applications, data mining tools, websites, etc. $16.57 USD (per hour)
ChIP-Seq Analysis $20.00 USD (per hour)
Metagenomic Analysis We provide Metagenomic Analysis services including data curation as well as analysis. $15.57 USD (per hour)
Genome Annotation $15.00 USD (per hour)
Variant Annotation We provide variant annotation services that include manual annotation of variants using public databases as well as annotation through automated pipelines/tools like GEMINI. $16.57 USD (per hour)

Geno-plex Bioinformatics Services

United States of America

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: 5

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 i... $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 i... 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 i... $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 i... $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 i... $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 i... $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 i... $150.00 USD (per sample)

Texas Genomics

NGS provider United States of America

This is a sample provider account. Do not actually order sequencing from this us.

Years in service: 6

Other services offered by Texas Genomics:

Service Description Price

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: 7

Other services offered by Parseq Lab:

Service Description Price

omics2view.consulting GbR

Germany

No other technology has been advancing the field of molecular biology and microbiology more in the last decade than next-generation sequencing (NGS). Facilitating analysis of genomic and transcriptomic material in ever more detail, NGS has become a versatile and indispensable method in ecological and medical research.

The omics2view.consulting GbR is an expert company in life science data mining. We offer high expertise in bioinformatics and biometric NGS-data analysis. Regardless of whether personalized, academic or clinical study, we can accompany your project from planing of the study design, via bioinformatic and statistical data analysis to publication of results in scientific journals. Our team combines professional consulting in NGS with high experience in diagnostics, molecular biology, (clinical) microbiology, ecology and life science.

Other services offered by omics2view.consulting GbR:

Service Description Price
Transcriptome Mapping Inquire
Other Services complex Statistics Inquire
Other Services Viromics Inquire
Other Services Amplicon analysis Inquire
Other Services Custom scripting Inquire
Other Services qPCR & FACS data Inquire
Other Services Molecular diagnostics Inquire
Other Services Metatranscriptomics Inquire
Exome Analysis Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Genome Annotation Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Variant Annotation Inquire
Microbiome Analysis 16s rNDA/rRNA Inquire

Sequencing.com

NGS provider United States of America

Sequencing.com is an online platform for storing and analyzing genetic data. Most services are free. This includes unlimited storage of genetic data and access to apps that turn genetic data into useful information.

Genetic Data Storage

  • Free storage of genetic data that is unlimited, secure and confidential

  • HIPAA and Safe Harbor compliant

  • Access your data 24/7

  • Store and analyze almost all human genetic data file formats (FASTQ, FASTA, SAM, BAM, VCF, gVCF, Clinical+ VCF, CRAM, etc.) from any testing technology

  • Securely share files with your colleagues and clients

  • You own your data - we store and protect it. We will never sell, rent or allow anyone else to access your data.

Apps

  • Apps analyze and process genetic data. For example, the free app EvE performs alignment, variant calling, annotation, interpretation and conversions for most genetic data files.

  • Many apps are free.

Years in service: 5

Other services offered by Sequencing.com:

Service Description Price
Other Services ADDITIONAL SERVICES * Genetic data storage * Custom software application (app) development * Custom application programming interfaces (APIs) * Custom algorithms for tertiary analysis (interpretation) of genetic data * Hosting for genomic software applications Genetic Data Storage * Free, unlimited storage of genetic data * Includes all file formats (FASTQ, FASTA, BAM, VCF, etc.) from any test... Inquire
Exome Analysis Apps available at Sequencing.com can analyze whole genome, exome and microarray data produced by most testing technologies. This includes FASTQ, FASTA, BAM/SAM, VCF and many other file formats. The EvE app is free and performs the following for human genetic data: * alignment * variant calling / discovery * annotation * interpretation * conversions Learn more about the EvE app: https://sequen... Inquire
Genome Mapping Note that this service is for genome alignment. Alignment and many other types of human genome analysis and interpretation can be accomplished using apps available at Sequencing.com. These apps can analyze whole genome, exome and microarray data produced by most testing technologies. This includes FASTQ, FASTA, BAM/SAM, VCF and many other file formats. The EvE app is free and performs the fol... Inquire
SNP / Indel Calling Variant calling, which includes SNP/InDel calling, can be accomplished for most human genetic data files using apps available at Sequencing.com. The EvE app is free and performs the following for human genetic data: * alignment * variant calling / discovery * annotation * interpretation * conversions Learn more about the EvE app: https://sequencing.com/eve Inquire
SNP/SV/CNV Discovery Apps available at Sequencing.com provide variant discovery, including SNP/SV/CNV discovery, for human genetic data. Apps can also be used to analyze whole genome, exome and microarray data produced by most testing technologies. This includes FASTQ, FASTA, BAM/SAM, VCF and many other file formats. The EvE app is free and performs the following for human genetic data: * pre-processing * alignmen... Inquire
Genome Annotation Apps available at Sequencing.com can annotate whole genome, exome and microarray data produced by most testing technologies. This includes FASTQ, FASTA, BAM/SAM, VCF and many other file formats. The EvE app is free and performs the following for human genetic data: * pre-processing * alignment * variant calling / discovery * annotation * interpretation * conversions Learn more about the EvE a... Inquire
Variant Annotation Apps available at Sequencing.com make it easy to perform variant annotation for human genetic data. Apps can also be used to analyze whole genome, exome and microarray data produced by most testing technologies. This includes FASTQ, FASTA, BAM/SAM, VCF and many other file formats. The EvE app is free and performs the following for human genetic data: * alignment * variant calling / discovery *... Inquire

ideas4biology Ltd.

Poland

DATA ANALYSIS Routine NGS data analysis in the area of genomics and transcriptomics, such as: - Gene expression and differential expression analysis - De novo and ab initio transcriptome assembly - Small RNA analysis - Genome variant calling and annotation

Customized tasks, including: - Identification of long noncoding RNAs - Identification of ta-siRNAs - Isomir and miRNA editing analysis - Annotation of non-model organisms - Building transcriptome-wide maps of RNA-RNA interactions

WORKSHOPS We offer workshops in a broad spectrum of bioinformatics applications, including: - RNA-Seq data analysis (4 days) - NGS in medical research (4 days)

EXPERIENCE We’ve been in the market since 2013 and came into collaboration with hundreds of customers. We’ve been working on model and non-model organisms, including viruses, bacteria, fungi, plants, animals, and human. We are part of research consortium aiming at development of personalized medicine services for diagnosis and treatment of lung cancers. We are also actively conducting research projects in different areas of genomics and transcriptomics, which gives us expertise in standard and up-to-date bioinformatics solutions.

INFRASTRUCTURE We have access to dedicated file storage and computational servers, with virtually unlimited (on demand) capacity.

Years in service: 5

Other services offered by ideas4biology Ltd.:

Service Description Price
Differential Gene Expression Analysis This includes: - quality filtering - adapter trimming - optionally: discarding rRNA-mapping reads or other contaminants - read mapping - expression estimation - differential expression analysis - a report, result data files and diagnostic plots Differential expression analysis itself, with expression estimations from customer: $30. $20.00 USD (per hour)
Transcriptome Mapping This includes: - quality check and filtering - adapter trimming - optional: discarding rRNA-mapping reads and other contaminants - read mapping (default or customized settings) - read mapping report and result files $20.00 USD (per hour)
Other Services Identification of long noncoding RNAs in animals and plants. This includes: - assessment of protein-coding potential with at least two independent methods - sequence length filtering - discarding of known, coding transcripts - discarding known noncoding RNAs other than lncRNAs - optionally: genomic context-driven filters - other filtering steps, depending on data availability, such as tr... $30.00 USD (per hour)
Read Filtering and Cleaning This includes: - Quality report - Quality filtering - Adapter trimming - Optionally: discarding rRNA-mapping reads or other contaminants $20.00 USD (per hour)
Small RNA Mapping This includes: - quality check and filtering - adapter trimming - read mapping to custom sequences (genome, transcriptome) - read mapping quality assessment - read mapping report This may be followed by miRNA identification or similar tasks, priced separately. $20.00 USD (per hour)
Genome Mapping This includes: - quality check and filtering - adapter trimming - optionally: discarding rRNA-mapping reads or other contaminants - read mapping with varied tools and settings - accomodated to customer's needs - quality report $20.00 USD (per hour)
SNP / Indel Calling This includes: - quality check and filtering - adapter trimming - read mapping and further processing of mapping results - SNP / Indel calling Both somatic and germline variants may be called. There is possibility to call structural variants as well, priced separately. $20.00 USD (per hour)
Small RNA Annotation This includes: - quality check and filtering - adapter trimming - read mapping to databases of noncoding RNAs, such as miRBase, DASHR or RFAM - annotation report $20.00 USD (per hour)
Methylation Analysis This includes: - quality check and filtering - adapter trimming - read mapping - calling methylated and unmethylated cytosines - differential methylation analysis: finding differentially methylated bases and regions $20.00 USD (per hour)
Transcriptome de novo Assembly This includes: - quality check and filtering - adapter trimming - optionally: discarding rRNA-mapping reads or other contaminants - transcriptome de novo assembly - a quality report and a transcriptome in FASTA format For further annotation of the transcriptome, please see our offer for "Transcriptome annotation". $20.00 USD (per hour)
Transcriptome Annotation This includes: - BLAST searches against databases of proteins and noncoding RNAs, including miRBase, RFAM, UniProt (Swiss-Prot) - hmmscan search against PFAM protein domains - assignment of GO terms to genes - assignment of KEGG pathways to genes - a report and annotation files with per gene details $20.00 USD (per hour)
Variant Annotation This includes: - prediction of possible consequences associated with predicted variants, such as affecting splicing of protein coding capacity - comparison with known variants from public databases - a report and result files $20.00 USD (per hour)

Igenbio.Inc

United States of America

Expertise:

  • Genome ORF calling: Eukaryotes and Prokaryote Genomes
  • Annotations
  • Pathway Analysis
  • Metabolic Reconstruction
  • SNP Analysis
  • Comparative Genomics
  • Integration of GWAS expression data onto genomes and pathways

Infrastructure:

Data is stored in house with a dedicated server room with 24/7 security. We compute using our proprietary algorithms internally and curate the genomes with comparative analysis platform. We have over 2,600 genomes in the data base which are manually curated. Access is provided via web or server access.

Other services offered by Igenbio.Inc:

Service Description Price
Comparative Genome Analysis Inquire
Custom scripting and special projects Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling Inquire
Genome Annotation Inquire
Methylation Analysis Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Whole Genome de novo Assembly Inquire

Diagnomics

United States of America

Diagnomics Inc. is a biotech company in the heart of the Biotech Beach, in San Diego California. The company focuses on products and services for personalized medicine based on personal genome and cutting edge bioinformatics analysis. Diagnomics provides complete personal genome sequencing and bioinformatics solutions to biomedical researchers, physicians and individuals seeking to understand the genetic influence of personal health and disease.

Expertise:

We aim to provide the highest possible quality genome sequencing service and annotation solutions from next generation sequencing (NGS) technology to guide personalized medicine based on an individuals' genetic information.

Infrastructure:

We are taking high-throughput computation and informatics seriously, and are constantly upgrading our server farm and softwares to enable cutting-edge bioinformatics for state-of-the-art genomic analysis. To that end, we house our infrastructure at a world class data center. Our server farm is located in San Diego, California at the ScaleMatrix facility.

Other services offered by Diagnomics:

Service Description Price
SNP / Indel Mapping Inquire
SNP / Indel Calling Inquire
Targeted Capture Analysis Inquire
Genome Annotation Inquire
Variant Annotation Inquire
Base Calling Inquire

intelliseq

Poland

I approach analytic challenges creatively with the result being novel, statistically significant and reproducible. I have high expertise on differential expression using RNA-seq.

Expertise:

I've been working with whole genome experiments for the last 10 years. I analysed more than 1000 gene expression microarrays (Illumina and Affymetrix, Human, Mouse, Rat and Pig). I analysed RNA-seq samples (total RNA and polyA RNA) from SOLiD 5500xl and Ion Proton, ChIP-seq samples from Illumina HiSEQ and DNA-seq (Exome) samples from Illumina HiSEQ. I developed several tools for functional analysis (see cremag.org) of gene lists.

Infrastructure:

I have almost unlimited access to Amazon EC2 and large server on site (two 8x core Xeon with 216 GB RAM 64GB of SAS disks)

Other services offered by intelliseq:

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
ChIP-Seq Analysis Inquire
Small RNA Mapping Inquire
SNP / Indel Mapping Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling Inquire
Genome Annotation Inquire
Methylation Analysis Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire

Genevia Technologies

Finland

Genevia Technologies provides a wide range of microarray and next generation sequencing data analyses, and bioinformatics services to life science companies and academia. In addition, we offer bioinformatics consulting projects at a fixed price, and genome-wide experiments done in collaboration with the top service providers.

Expertise:

Our expertise is in handling multiple microarray (expression, copy number, ChIP, methylation, etc) and next-gen sequencing (DNA-seq, RNA-seq, MeDIP-seq, ChIP-seq, GRO-seq, etc) data simultaneously and effectively, and combining them with other data such as clinical variables or pathway information. We have experience in most common mammalian systems, but especially in multiple human cancers. We have also worked on data from multiple species of lower eucaryotes and bacteria.

Infrastructure:

We have access to dedicated file storage servers, a computing cluster, a computing grid (of over 1000 CPUs), and cloud computing capabilities.

Visit our homepage to read more about us and our bioinformatics as a service: www.genevia.fi

Other services offered by Genevia Technologies:

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

Biosof LLC

United States of America

Expertise:

Expertise in mainly with plant genomes (wheat, tomato, potato, tobacco, rice, maize, diatoms and arabidopsis).

Infrastructure:

Access to over 800 cores (2.3Ghz and faster) SMP compute cluster. Access to over 50TB of raw storage. Computing infrastructure includes all commonly used bioinformatics software and databases. All computing infrastructure is maintained by a 24/7 IT service.

Other services offered by Biosof LLC:

Service Description Price
Differential Gene Expression Analysis Inquire
Comparative Genome Analysis Inquire
Custom scripting and special projects Inquire
Read Filtering and Cleaning Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Genome Annotation Inquire
Transcriptome de novo Assembly Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Whole Genome de novo Assembly Inquire

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

H3Me Life Sciences

India

Our focus:

  1. Routine NGS Analysis for resequencing / model organism based projects. This includes variant calling and annotation, Transcriptome (both mRNA and small RNA) assembly; differential expression and annotation for model organisms, targeted capture analyses (ChIP-seq, and MeDIP-seq), methylation (BS-seq), and metagenomics.

  2. Development of custom methods and special projects for non-model organisms.

Expertise:

Expertise in variant calling, expression profiling, targeted capture analysis, gene annotation in novel genomes and method development. Have worked on data from the following organisms:

  • Human
  • Mouse
  • Bacteria
  • Plants (Azadirachta indica, Santalum album, Oryza sativa)
  • Walleye Fish
  • Mangrove tree (de novo transcriptome assembly)
  • Planaria worm (method development for annotating poly-adenylation sites via 3P sequencing)

Infrastructure:

For clients in India, we have a server cluster; with each node having 16GB of RAM and 4 TB of HDD. Collectively, we have 48TB of HDD space. For international clients we provide analysis on the cloud (AWS).

Other services offered by H3Me Life Sciences:

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

Cytognomix Inc.

Canada

Genome-scale interpretation and annotation of non-coding mutations in the human genome. Emphasis on mRNA splicing mutations affecting natural and regulatory sites. RNA binding protein (UTR) and transcription factor binding site mutation analyses are also available under special arrangement.

Expertise:

Expertise in non-coding mutation analysis. Homo sapiens, mus musculus.

Infrastructure:

We have a 128 node compute cluster, several I7-based Linux and PC workstations and an iMac. Our data and results are made available through a commercial website managed by our company.

Other services offered by Cytognomix Inc.:

Service Description Price
Genome Annotation 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
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

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.

  • ur 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: 7

Other services offered by DREAMgenics:

Service Description Price
Differential Gene Expression Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome Mapping 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
Read Filtering and Cleaning https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Exome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
ChIP-Seq Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Small RNA Mapping https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
SNP / Indel Mapping 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
SNP / Indel Calling 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
Genome Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Small RNA Annotation https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Methylation Analysis https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome de novo Assembly https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Transcriptome Annotation 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
Base Calling https://www.dreamgenics.com/en/bioinformatics-services/ Inquire
Microbiome Analysis https://www.dreamgenics.com/en/bioinformatics-services/ 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: 8

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)

Rajesh Mahato

India

Next Generation Sequencing (NGS) is a key technological tool that has emerged in the past decades. NGS is known to provide a cost-effective and time-saving technological advancement in nucleotide sequencing activities, and has found its application in several sectors of the life-sciences domain at large. At ArrayGen, we focus on developing niche NGS data analysis tools, protocols, and custom workflows, which can expedite your research. We also provide data analysis services where we draw meaningful insights from standard or custom raw nucleotide sequence data.

ArrayGen specializes in Genomics data analysis and research, as we believe in the level of precision, predictability, benchmark-ability, and data analysis capability of genomics data over other forms of biological data. ArrayGen constantly strives to develop new solutions, and plug the existing gaps in the technological advancement of the field.

Expertise:

We have worked with wide variety of organism like Human, Arabidopsis, viral and bacterial genomes which provide us expertise in analysing NGS data.

Infrastructure:

We have our own in-house server as well as we also provide FTP access to our storage server to upload raw data and download analyzed data.

Years in service: 5

Other services offered by Rajesh Mahato:

Service Description Price
Differential Gene Expression Analysis Read Quality Report before and after trimming,Mapping report,Differential expressed Genes(Upregulated & Downregulated),Functional analysis(GO & Pathway), GO and Pathway Enrichment analysis report,heatmap and volcano plots, Pathway network analysis report,custom analysis as per the client request $200.00 USD (per sample)
Transcriptome Mapping Complete mapping reports $50.00 USD (per sample)
Comparative Genome Analysis comparative analysis/syntenic region detection/vizualization $150.00 USD (per sample)
Custom scripting and special projects Complete Algorithm detection/GUI database or software for biologist/Automated scripts pipeline for NGS data analysis to process larger datasets/Any algorithm as per the paper published Inquire
Other Services We provide software development/shell scripts for your NGS data analysis as per your requirement. This will save time and money if you would like to perform any number of Data analysis. Inquire
Other Services We also provide complete custom microarray chip designing, microarray data analysis and other bioinformatics services Inquire
Other Services ArrayGen also provides complete Industrial based training in all NGS applications - RNASeq/DNASeq/Chipseq/metagenomics/WGS denovo assembly/Methylseq/LncRNA etc please visit at www.arraygen.com to know more details Inquire
Other Services ArrayGen also provides complete custom training with your own datasets in all NGS applications - RNASeq/DNASeq/Chipseq/metagenomics/WGS denovo assembly/Methylseq/LncRNA etc please visit at www.arraygen.com to know more details Inquire
Other Services ArrayGen also provides Internship(1/2/3/4/6/12 months) as well as 6 months BICP Industrial for more in depth exposure with bioinformatics program- RNASeq/DNASeq/Chipseq/metagenomics/WGS denovo assembly/Methylseq/LncRNA etc please visit at www.arraygen.com to know more details Inquire
Read Filtering and Cleaning Read filtering Quality report before and after trimming and cleaning $50.00 USD (per sample)
ChIP-Seq Analysis Read Quality Report before and after trimming,Peak enriched report,Peak annotation report,Visualization of enriched peaks,Motif analysis report, Custom analysis as per the client requirement, Also complete Industrial training with custom data available till publication support $150.00 USD (per sample)
Small RNA Mapping miRNA reads mapping report(SAM/BAM) and mapping summary $50.00 USD (per sample)
SNP / Indel Mapping Mapping reports(SAM/BAM) $50.00 USD (per sample)
Metagenomic Analysis Read Quality Report before and after trimming, OTUs identification & Functional,Taxonomic composition and relative abundance,Diversity report,Class/phylum frequency,Heatmap, phylogenetic, Alpha & Beta diversity, custom analysis as per the client request $200.00 USD (per sample)
SNP / Indel Calling All SNP/Indel called report $50.00 USD (per sample)
SNP/SV/CNV Discovery Complete SNP/CNV/SV detection from sequencing data $250.00 USD (per sample)
Targeted Capture Analysis Read Quality Report before and after trimming,Mapping report,variation mutation report,variation annotation,mutation visualization,custom analysis as per client request $150.00 USD (per sample)
Genome Annotation Gene/orf prediction,Functional Annotation(GO and pathway),Visualization/custom analysis $150.00 USD (per sample)
Small RNA Annotation Target Gene prediction and Functional annotation/ miRbase miRNA reference annotation/ functional analysis GO and pathway enrichment for know and novel miRNA $150.00 USD (per sample)
Methylation Analysis Read Quality Report before and after trimming,Mapping report,Methylated and unmethylated regions,Differential methylated regions, Annotation,vizualization,custom analysis as per client request $150.00 USD (per sample)
Transcriptome de novo Assembly Raw data QC, Transcript assembled sequence and statistics report, Differential Gene Expression(UpRegulated & DownRegulated), Gene Prediction & functional annotation, GO and pathway enrichment analysis report, different plots(heatmap,volcano plots etc), Pathway network analysis and complete custom support. $200.00 USD (per sample)
Transcriptome Annotation Functional annotation Gene ontology and pathway / gene feature assignment $50.00 USD (per sample)
Variant Annotation Complete variations annotation like gene feature/OMIM/polyphen & sift score/upstream & downstream etc $100.00 USD (per sample)
Whole Genome de novo Assembly Read Quality Report before and after trimming,Assembly and statistics report,Repeat masking,Gene prediction and functional annotation,Vizualization using circos,custom analysis as per client request $200.00 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: 9

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: 7

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: 13

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)

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: 4

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 $20.00 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: 6

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)

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)

TheragenEtex

NGS provider South Korea

TheragenEtex is specialized genomics company developing innovative diagnosis tools and new drugs using the genomics and bioinformatics technologies. TheragenEtex's world class analysis technologies are proven by number of high impact journal publications.

We are providing genome-based customized research service such as Genome, Transcriptome and Epigenome. In addition, we have personal genome service which is screening disease susceptibility, physical traits, drug sensitivity and so on.

Based on these technologies and experiences, we are putting endless efforts to revolutionize personalized medicine and to become a global leader in human welfare and healthcare.

Years in service: 10

Other services offered by TheragenEtex:

Service Description Price
SNP / Indel Calling Inquire
Variant Annotation Inquire

Meghagen Biosciences Private Limited

NGS provider India

MeghaGen, is a life sciences company providing end-to-end services for NGS sequencing and data analysis.

*We have established and implementing highly scalable pipelines to help researchers with their NGS-related data analysis.

*We help in processing, analyzing and interpreting all application areas spawned by NGS technologies. For example, --Detection of variants in the genomes of all organisms with reference genomes including human, plants, animals and microbes. --RNA-sequencing to detect expression levels of gene, splice variants, lincRNA and miRNA that correlate with a given biological context --Exome and targeted sequencing to discover actionable genetic variants for medical applications. --Microbiome profiling using 16s rRNA or whole-genome metagenome. --Epigenetic changes in biological contexts using ChIP-seq, Methyl-seq, BS-seq. --De novo sequencing and assembly of genomes or organism without a reference.

*We can work together to develop the analysis pipelines for any customized applications that you might conceive using cutting edge cloud computing.

*Analysis comes with publication-ready plots and tables.

*MeghaGen uses AWS cloud based platform that is super-optimized for data analysis and data archival.

*We strive to ensure that our clients enjoy the highest quality and most cost-effective bioinformatics solutions.

Years in service: 4

Other services offered by Meghagen Biosciences Private Limited:

Service Description Price
Differential Gene Expression Analysis $150.00 USD (per sample)
Transcriptome Mapping $135.00 USD (per sample)
Comparative Genome Analysis $300.00 USD (per sample)
Custom scripting and special projects Inquire
Other Services Inquire
Read Filtering and Cleaning $30.00 USD (per sample)
Exome Analysis Inquire
ChIP-Seq Analysis $150.00 USD (per sample)
Small RNA Mapping $120.00 USD (per sample)
SNP / Indel Mapping $150.00 USD (per sample)
Genome Mapping $120.00 USD (per sample)
Metagenomic Analysis Inquire
SNP / Indel Calling $120.00 USD (per sample)
SNP/SV/CNV Discovery $300.00 USD (per sample)
Targeted Capture Analysis $125.00 USD (per sample)
Genome Annotation $1250.00 USD (per sample)
Small RNA Annotation $300.00 USD (per sample)
Methylation Analysis Inquire
Transcriptome de novo Assembly $2000.00 USD (per sample)
Transcriptome Annotation $1000.00 USD (per sample)
Variant Annotation $100.00 USD (per sample)
Whole Genome de novo Assembly $3500.00 USD (per sample)
Base Calling Inquire
Microbiome Analysis Inquire

Leucine Rich Bio

India

Leucine Rich Bio has been selected as the award recipient for the"2016 Frost & Sullivan India Award for Enabling Technology in the Cloud-enabled Genomics Industry, APAC"

Leucine Rich Bio Private Limited is a Bioinformatics driven company based in the Silicon Valley of India, Bangalore, specializing in Next Generation Sequencing (NGS) Data Analysis & Interpretation. Our area of focus is in Human Genome Interpretation, especially for clinical and research use. We use advances in the area of Computer Science, Information Science, Data Management, Statistics and Systems Biology to solve complex problems in Genomics. We envision using cutting edge big data approaches along with machine learning algorithms to delve deeper into the understanding of the human genome and develop novel solutions to drug discovery.

At Leucine Rich Bio we have in-depth knowledge on Cancer Genomics, Genetic Conditions caused by Rare Variants and Drug Response. We have collated information on Genetic Variants, Mendelian Inheritance, Genome Wide Association Studies and Pharmacogenomics data. Our in-house curated database (LRB – Human Genome Variation Database) is developed that cross-checks all information with the original scientific literature to ensure data is accurate, clinically relevant and up to date. The database provides functional information, mutation impact on disease, drug response and variant impact on protein structure and functions, with its relevant references.

Our pipelines are tailored to accurately generate a report in a clinically relevant time frame. Our proprietary platform AGIS based customized report translates complex genomic data into clinically relevant and actionable biological information. At Leucine Rich Bio we help clinicians appreciate the value of Personalized Medicine. Our in house curated database LRB-HGVD is tailored to provide variant functional information to AGIS

Our dynamic genome interpretation service provides researchers in pharmaceutical industry and top research labs worldwide with choice of bioinformatics suite to interpret, analyse and act on relevant information derived from ever evolving NGS data.

Other services offered by Leucine Rich Bio:

Service Description Price
Differential Gene Expression Analysis Inquire
Transcriptome Mapping Inquire
Comparative Genome Analysis Inquire
Custom scripting and special projects Inquire
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)
Exome Analysis Inquire
ChIP-Seq Analysis Inquire
SNP / Indel Mapping Inquire
Genome Mapping Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling Inquire
SNP/SV/CNV Discovery Inquire
Targeted Capture Analysis Inquire
Genome Annotation Inquire
Small RNA Annotation Inquire
Transcriptome de novo Assembly Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Whole Genome de novo Assembly Inquire
Microbiome Analysis 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

genexa Ltd

Switzerland

genexa is a genomic data analysis provider located in Switzerland. Our bioinformatics services are centered around de novo assembly of genomes and metagenomes. We focus on processing, analysis, and interpretation of your genomics data. For all our fields of expertise, we offer to perform the entire analysis workflow from raw data to documentation, but also consulting and troubleshooting if required. genexa also provides resources to run computationally demanding tasks for specific jobs if you have an existing analysis workflow, but lack the computational resources to run it on large amounts of data. For further information check: genexa.ch

Years in service: 4

Other services offered by genexa Ltd:

Service Description Price
Differential Gene Expression Analysis Inquire
Comparative Genome Analysis Inquire
Custom scripting and special projects Inquire
Other Services We offer bioinformatics services using long-read sequencing (PacBio & Oxford Nanopore Technologies). We have several years of experience using third-gen. technologies, mainly applying these technologies for de novo assembly of individual genomes and metagenomes. We also offer transcriptomic analyses using long-read technologies. If you want to start using PacBio or Oxford Nanopore Technologie... Inquire
Read Filtering and Cleaning Inquire
Metagenomic Analysis Inquire
SNP / Indel Calling Inquire
Genome Annotation Inquire
Transcriptome Annotation Inquire
Variant Annotation Inquire
Whole Genome de novo Assembly Inquire
Base Calling Inquire
Microbiome Analysis Inquire

World Fusion US

United States of America

World Fusion is a well-established bioinformatics and cheminformatics software developer and services supplier with offices in Japan and the US. We have been at the forefront of developing genomic and drug discovery research tools since our early work on the Human Genome Project, and offer unparalleled reliability and expertise in our services.

Our customizable services include NGS data analysis, in-silico research services, and we are annotation specialists offering the most comprehensive correlations between genes, proteins, diseases, and chemicals.

The majority of the information is generated from our proprietary genomic and drug discovery research platform and knowledge base that we have been upgrading and building upon for over 10 years. It is comprised of original in-house data, curated information from over 60 top public data sets, and a chemical dictionary containing over 75 million non-redundant chemical compounds.

Our more recently added metagenomic and metaranscriptomic analysis services are carried out using state-of-the-art, original in-house software applications.

We offer MANY additional services, please contact us about your specific needs.

Years in service: 13

Other services offered by World Fusion US:

Service Description Price
Other Services Target prediction from chemical structure - prediction of target proteins which is based on: 1.5M compounds, 5500 protein, and 5M interactions. Inquire
Other Services In-silico target exploration from disease - therapeutic targets, related drugs, gene and protein targets, etc. Includes an extensive annotation table with information about the disease and related diseases, SNPs, compounds, drugs, genes, proteins, and tissues. Inquire
Other Services Target Prioritization helps with the selection of gene/proteins for your research, from gene expression/SNV data - the analysis provides information about compounds and the activities, assays, SNPs, diseases, domains, pathways, and references. Inquire
Metagenomic Analysis Analysis of the transcripts present in the RNA-seq data through frequency analysis of functional categories from the selected protein DB (such as COG). Result files include annotations from ligand information with related chemical compounds, pathways, and iPath. •Biological function information •Metabolic compound info from proteins •Multiple sample analysis •Bar charts, pie charts, and ... Inquire
Metagenomic Analysis 16S/28S/ITS rRNA metagenomic data analysis of the composition and diversity of microbial or fungal species from natural environments. Interactive HTML report with taxonomically classified charts & graphs, read counts, 2D, 3D, and interactive PCA plots, heat clustering maps, and self-organizing maps. •Metagenomic analysis of bacteria from species classification of taxonomic rank •Fungal met... Inquire
Genome Annotation Gene/Protein Annotation Services: • Identify relationships beween genes and proteins or diseases • Cite connections between genes or proteins and chemicals • Extract bind/inhibit chemicals from proteins or genes • Examine SNP information and association with disease • Find bind/inhibit compounds and therapeutic targets from associated disease • Gene expression prioritization from RNAseq d... Inquire
Transcriptome Annotation Expression data analysis includes over 20 kinds of annotation such as: genes (ontology, pathways), proteins, diseases, domains, ligands, and compounds. Prioritization of genes and proteins can be executed from a variety of directions. •Statistical processing from expression values •Conversion and active compound information from proteins •Inhibitor compounds and inhibitory active compound... Inquire
Variant Annotation Analysis focuses on the SNP variant amino acid change and includes annotations of related diseases, genes, proteins, assays, ligands, SNPs, domains, and chemical compounds (active compound information, crystal structure, chemical formula, activities, etc.). •Non-synonomous SNPs and chemicals influenced by mutation location •Information about the compounds and proteins affected by the amino... Inquire