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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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JBrowse Resource Report Resource Website 10+ mentions |
JBrowse (RRID:SCR_001004) | JBrowse | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. | genome |
is used by: Genome Resources for Yeast Chromosomes is listed by: OMICtools is listed by: Debian has parent organization: Broad Institute |
NHGRI 5R01HG004483-09 | PMID:22517427 PMID:21221095 |
GNU Lesser General Public License, Account required | OMICS_00918 | https://sources.debian.org/src/jbrowse/ | SCR_001004 | 2026-09-12 12:55:17 | 32 | |||||
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Golden Helix GenomeBrowse Resource Report Resource Website 1+ mentions |
Golden Helix GenomeBrowse (RRID:SCR_001213) | GenomeBrowse | commercial organization, data processing software, data visualization software, software application, software resource | Software tool that delivers visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an user interface to make sure that your discovery process is fluid and streamlined. | Golden Helix, variant, visualization, genome |
is listed by: OMICtools has parent organization: Golden Helix Incorporated |
Free, Available for download, Freely available | OMICS_02129 | SCR_001213 | 2026-09-12 12:55:21 | 2 | ||||||||
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GenoViewer Resource Report Resource Website |
GenoViewer (RRID:SCR_001203) | GenoViewer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Open source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data. | next-generation sequencing, sequence, mutation, windows, linux, mac os x, genome, browser, sam, bam, fasta, gff, read error, snp, mnp, insertion, deletion | is listed by: OMICtools | PMID:22359445 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02146 | https://github.com/astrid/GenoViewer | SCR_001203 | 2026-09-12 12:55:21 | 0 | ||||||
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GenoMiner Resource Report Resource Website |
GenoMiner (RRID:SCR_001202) | GenoMiner | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A next generation sequencing data analysis computer for biologists with or without IT background. It has an easy to-use graphical interface to analyze sequencing data in with only 15 clicks. A range of standard, add-on and custom applications help analyze and visualize data generated by Next Generation Sequencing machines. These are installed on each GenoMiner by default: * Reference assembly * De novo assembly * ChiP-Seq * BLAST * Hybrid de novo assembly * Hybrid reference assembly Add-on applications: * Quality assesment * RNA-Seq * Copy Number Variation (CNV) * Multiple Sequence Alignment * miRNA-Seq * Variant Calling | next-generation sequencing, reference assembly, de novo assembly, chip-seq, blast, hybrid de novo assembly, hybrid reference assembly, genome, computer, hardware, instrument, equipment | is listed by: OMICtools | PMID:16267081 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02149 | http://www.astridbio.com/genominer.html | SCR_001202 | GenoMiner: Genome Analyzer | 2026-09-12 12:55:21 | 0 | |||||
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PeakAnalyzer Resource Report Resource Website 1+ mentions |
PeakAnalyzer (RRID:SCR_001194) | PeakAnalyzer | software resource | A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution. | genome, chip, signal peak, binding site, modification site, enrichment loci, peak region, sequence, motif, chip-seq, chip-chip, c++, java, linux, mac os x, windows, bed, gtf, annotation, r, high-throughput sequencing, chromatin binding, modification loci, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:20691053 | Free, Available for download, Freely available | biotools:peakanalyzer, OMICS_02156 | https://bio.tools/peakanalyzer | SCR_001194 | 2026-09-12 12:55:21 | 3 | ||||||
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Breakway Resource Report Resource Website |
Breakway (RRID:SCR_001180) | Breakway | software resource | A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives. | genome, structural variation, breakpoint |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at Los Angeles; California; USA |
PMID:20126413 | Free, Available for download, Freely available | OMICS_02176 | SCR_001180 | Breakway: Identify Structural Variations in Genomic Data | 2026-09-12 12:55:20 | 0 | ||||||
|
ChIP-seq Resource Report Resource Website 5000+ mentions |
ChIP-seq (RRID:SCR_001237) | ChIP-seq | data analysis software, data processing software, software application, software resource, software toolkit | Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface. | high-throughput sequencing, chromatin immuno precipitation, chip-seq, genome, c |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:27863463 | Free, Available for download, Freely available | OMICS_02103 | https://epd.expasy.org/chipseq/, https://chip-seq.sourceforge.net/ | SCR_001237 | ChIP-seq - Tools for the analysis of ChIP-seq data | 2026-09-12 12:55:21 | 8035 | |||||
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Patchwork Resource Report Resource Website 10+ mentions |
Patchwork (RRID:SCR_000072) | Patchwork | software resource | Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data. | genome, allele, copy number, bam, unix, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Uppsala University; Uppsala; Sweden |
Cancer, Tumor | PMID:23531354 | Free, Available for download, Freely available | biotools:patchwork, OMICS_02118 | https://bio.tools/patchwork | SCR_000072 | 2026-09-12 12:55:02 | 10 | |||||
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Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, software resource, web service | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK062434; NIDDK DK074967 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root, https://bio.tools/cistrome | SCR_000242 | Galaxy Cistrome | 2026-09-12 12:55:05 | 17 | |||||
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UnSplicer Resource Report Resource Website 1+ mentions |
UnSplicer (RRID:SCR_000226) | software resource | An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight. | RNA, sequencing, alignment, short reads, genome, genemark-es, gene prediction |
is listed by: OMICtools has parent organization: Georgia Institute of Technology; Georgia; USA |
PMID:24259430 | Free, Available for download, Freely available | OMICS_01806 | SCR_000226 | 2026-09-12 12:55:05 | 1 | ||||||||
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ChromasPro Resource Report Resource Website 10+ mentions |
ChromasPro (RRID:SCR_000229) | data acquisition software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available. | genome, sequence, dna, assemble, data, illumina, next gen sequence, next generation | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01808 | SCR_000229 | 2026-09-12 12:55:05 | 14 | ||||||||||
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Opal Research Resource Report Resource Website 1+ mentions |
Opal Research (RRID:SCR_000405) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed. | sequence analysis software, genome interpretation, variant prioritization, disease gene prioritization, next-generation sequencing, clinical interpretation, clinical genomics software, genome, protein function, disease, genomic variant, mutation | is related to: VAAST | PMID:23895124 | Restricted | SciRes_000140 | SCR_000405 | Omicia Opal Research, Omicia Opal, Opal Research Variant Interpretation | 2026-09-12 12:55:08 | 1 | |||||||
|
MuTect Resource Report Resource Website 100+ mentions |
MuTect (RRID:SCR_000559) | MuTect | software resource | Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. | next-generation sequencing, somatic mutation, tumor, normal, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Cancer | PMID:23396013 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mutect, OMICS_00087 | https://bio.tools/mutect | SCR_000559 | Mutect | 2026-09-12 12:55:11 | 102 | ||||
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Reprever Resource Report Resource Website |
Reprever (RRID:SCR_000463) | Reprever | software resource | Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number. | genomics, genomic region, insertion breakpoint, insertion, breakpoint, duplicon, genome |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at San Diego; California; USA |
PMID:23658221 | Free, Available for download, Freely available | OMICS_01561 | SCR_000463 | Reprever: resolving low-copy duplicated sequences using template drive | 2026-09-12 12:55:10 | 0 | ||||||
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UCSCin Resource Report Resource Website |
UCSCin (RRID:SCR_000571) | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Beta software used to align and browse a genome. | genome | has parent organization: University of Toronto; Ontario; Canada | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144379 | SCR_000571 | 2026-09-12 12:55:11 | 0 | |||||||||
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wANNOVAR Resource Report Resource Website 10+ mentions |
wANNOVAR (RRID:SCR_000565) | wANNOVAR | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotate, function, genetic variant, high-throughput sequencing, single nucleotide variant, gene, variant, allele frequency, mutation, annotation, genome, insertion, deletion |
is listed by: OMICtools is related to: ANNOVAR has parent organization: University of Southern California; Los Angeles; USA |
PMID:22717648 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00194 | SCR_000565 | 2026-09-12 12:55:11 | 22 | |||||||
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Computational Cancer Genomics Group Resource Report Resource Website 1+ mentions |
Computational Cancer Genomics Group (RRID:SCR_000772) | data analysis software, data or information resource, data processing software, database, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB). | eukaryotic, expression, function, gene, analyzer, annotation, biological, clustering, computational, data, genome, in vitro, mapping, messengerrna, molecular, mpss, mrna, one-dimensional, organism, promoter, sage, sequence, snp, software, tag, technology, tool, transcription, transcriptome | has parent organization: SIB Swiss Institute of Bioinformatics | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25561 | SCR_000772 | CCG | 2026-09-12 12:55:14 | 3 | ||||||||
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GEUVADIS Resource Report Resource Website 1+ mentions |
GEUVADIS (RRID:SCR_000684) | GEUVADIS | consortium, data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genetic, variation, health, disease, medical, sequencing, high-throughput sequencing, human genome, genome, genomics, personalized medicine, genomic medicine | is listed by: OMICtools | European Union ; FP7 ; HEALTH |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01779, SCR_013706 | SCR_000684 | Genetic European Variation in Health and Disease - A European Medical Sequencing Consortium, GEUVADIS Consortium, Genetic European Variation in Health and Disease | 2026-09-12 12:55:13 | 1 | ||||||
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EUCOMMTOOLS Resource Report Resource Website 1+ mentions |
EUCOMMTOOLS (RRID:SCR_000676) | EUCOMMTOOLS | biomaterial manufacture, material service resource, production service resource, service resource | Functional Annotation of the Mouse Genome, it will complete the International Knockout Mouse Consortium (IKMC) resource of mutations for all protein coding genes. Furthermore, it will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines. In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource. EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide: EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Knockout-first Mutant Alleles: EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an "artificial intron", containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene. Cre Resources: EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources. Research, Technology and Complementary Reagents: EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include: * Development of novel recombinase based regulatory switches * Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes * Development and validation of complementary modular vector reagents which enable the construction of new useful knock-in alleles such as fluorescent and other reporters, site specific recombinases, and mutant cDNAs. These novel alleles can be constructed either by re-utilizing existing IKMC modular vector resources or directly modifying existing targeted IKMC ES cell lines by RMCE. | genome, annotation, function, mutation, protein coding gene, vector, mutant embryonic stem cell, mutant mouse strain, cre driver, cre, recombinase, c57bl/6, allele, embryonic stem cell line, c57bl/6n, knock-in |
uses: EuMMCR uses: European Mouse Mutant Archive is related to: Recombinase (cre) Activity has parent organization: International Knockout Mouse Consortium |
European Union ; FP7 ; THEME Health |
nlx_152804 | SCR_000676 | EUCOMM - Tools for Functional Annotation of the Mouse Genome, EUCOMM: Tools for Functional Annotation of the Mouse Genome | 2026-09-12 12:55:13 | 1 | |||||||
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MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Burroughs-Wellcome Fund ; Japan Society for the Promotion of Science ; NHGRI HG002096; NHGRI HG006039; NIGMS R01GM126567; NIGMS R35GM139504; NSF ABI 1661218 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-09-12 12:55:13 | 2774 |
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