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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NCBI Sequence Read Archive (SRA) Resource Report Resource Website 5000+ mentions |
NCBI Sequence Read Archive (SRA) (RRID:SCR_004891) | SRA | data or information resource, data repository, database, service resource, storage service resource | Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them. | sequence, blast, next-generation sequence, alignment, read placement, reference sequence, roche 454 gs system, illumina genome analyzer, applied biosystems solid system, helicos heliscope, complete genomics, pacific biosciences smrt, high-throughput sequencing, data analysis service, gold standard |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is listed by: OMICtools is related to: European Nucleotide Archive (ENA) is related to: RecountDB is related to: SRAdb is related to: DDBJ Sequence Read Archive is related to: Bgee: dataBase for Gene Expression Evolution is related to: NCBI BioSample is related to: DDBJ Sequence Read Archive is related to: METAGENOTE has parent organization: NCBI works with: SARS-CoV-2-Sequences works with: Signaling Pathways Project |
NLM | PMID:22009675 PMID:21062823 |
Free, Available for download, Freely available | OMICS_01031, nlx_86174, r3d100010775 | https://doi.org/10.17616/R31S69 | SCR_004891 | Sequence Read Archive, , SRA, NCBI SRA | 2026-08-29 11:22:02 | 7247 | ||||
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cortex var Resource Report Resource Website 1+ mentions |
cortex var (RRID:SCR_005081) | cortex_var | software resource | A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal). cortex_var features * Variant discovery by de novo assembly - no reference genome required * Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them. * Capable of calling SNPs, indels, inversions, complex variants, small haplotypes * Extremely accurate variant calling - see our paper for base-pair-resolution validation of entire alleles (rather than just breakpoints) of SNPs, indels and complex variants by comparison with fully sequenced (and finished) fosmids - a level of validation beyond that demanded of any other variant caller we are aware of - currently cortex_var is the most accurate variant caller for indels and complex variants. * Capable of aligning a reference genome to a graph and using that to call variants * Support for comparing cases/controls or phenotyped strains * Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM | genome assembly, variation analysis, sequence, variation, genotype variant, haploid, diploid, snp, indel, inversion, variant, haplotype, de novo assembly, genotyping, variant-calling, population analysis, population assembly |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:22231483 | GNU General Public License, v3, Acknowledgement requested | OMICS_00056 | SCR_005081 | cortex_var - for variant and population assembly | 2026-08-29 11:22:06 | 3 | ||||||
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European Genome phenome Archive Resource Report Resource Website 500+ mentions |
European Genome phenome Archive (RRID:SCR_004944) | EGA | data access protocol, data or information resource, data repository, data set, service resource, software resource, storage service resource, web service | Web service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication. | phenomenon, trait, sequence, genotype, experiment, case-control, population, family study, snp, cnv, phenotype, genomic, gold standard, bio.tools |
is used by: Blueprint Epigenome is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases lists: METABRIC is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:34791407 | Restricted | BioTools:ega, biotools:ega, r3d100011242, OMICS_01028, nlx_91316 | https://ega-archive.org/, https://bio.tools/ega, https://bio.tools/ega, https://doi.org/10.17616/R3W619 | SCR_004944 | , The European Genome-phenome Archive, The European Genome-phenome Archive (EGA), EGA | 2026-08-29 11:22:13 | 787 | |||||
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NCBI Popset Resource Report Resource Website 1+ mentions |
NCBI Popset (RRID:SCR_005049) | PopSet | data or information resource, data repository, database, service resource, storage service resource | Database containing a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. Users may submit a Popset using Sequin. | nucleotide sequence, nucleotide, sequence, dna sequence, dna, evolution, population, genomics, eukaryotic cell, mutation, phylogenetic, ecosystem, gold standard |
is listed by: re3data.org has parent organization: NCBI |
nlx_99613, r3d100010777 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=popset, https://doi.org/10.17616/R3S901 | SCR_005049 | Entrez PopSet | 2026-08-29 11:22:14 | 9 | |||||||
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M-pick Resource Report Resource Website |
M-pick (RRID:SCR_004995) | M-pick | software resource | A modularity-based clustering software for Operational Taxonomic Unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance or variance levels to define OTUs. | 16s rrna sequence, 16s rrna, rrna, sequence, binning |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
OMICS_01447 | SCR_004995 | M-pick: a modularity-based clustering method for OTU picking | 2026-08-29 11:22:04 | 0 | ||||||||
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Classifier for Metagenomic Sequences Resource Report Resource Website 100+ mentions |
Classifier for Metagenomic Sequences (RRID:SCR_004929) | ClaMS | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd, 2023. Sequence composition based classifier for metagenomic sequences. It works by capturing signatures of each sequence based on the sequence composition. Each sequence is modeled as a walk in a de Bruijn graph with underlying Markov chain properties. ClaMS captures stationary parameters of the underlying Markov chain as well as structural parameters of the underlying de Bruijn graph to form this signature. In practice, for each sequence to binned, such a signature is computed and matched to similar signatures computed for the training sets. The best match that also qualifies the normalized distance cut-off wins. In the case that the best match does not qualify this cut-off, the sequence remains un-binned. | metagenome, classification, sequence |
is listed by: OMICtools has parent organization: DOE Joint Genome Institute |
DOE contract DE-AC02-05CH11231 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_005519, nlx_144629, OMICS_01452 | SCR_004929 | 2026-08-29 11:22:13 | 150 | |||||||
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RetroSeq Resource Report Resource Website 10+ mentions |
RetroSeq (RRID:SCR_005133) | RetroSeq | software resource | A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences. | mobile element insertion, next-gen sequencing, bam, transposable element, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:23233656 | Acknowledgement requested, Open unspecified license | OMICS_11232, OMICS_00120 | SCR_005133 | 2026-08-29 11:22:08 | 46 | |||||||
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SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | analysis service resource, data analysis service, production service resource, service resource, software resource | A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. | annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA has parent organization: SourceForge |
PMID:20854673 | GNU General Public License, v2 | OMICS_00182 | SCR_005186 | SeqAnt - Sequence Annotator | 2026-08-29 11:22:23 | 2 | ||||||
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GASVPro Resource Report Resource Website 1+ mentions |
GASVPro (RRID:SCR_005259) | GASVPro | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool combining both paired read and read depth signals into probabilistic model which can analyze multiple alignments of reads. Used to find structural variation in both normal and cancer genomes using data from variety of next-generation sequencing platforms. Used to predict structural variants directly from aligned reads in SAM/BAM format.Combines read depth information along with discordant paired read mappings into single probabilistic model two common signals of structural variation. When multiple alignments of read are given, GASVPro utilizes Markov Chain Monte Carlo procedure to sample over the space of possible alignments. | structural variation, genome, genomics, alignment, sequencing, variant, variation, detection, dna, paired, end, read, sequence |
is listed by: OMICtools is related to: GASV has parent organization: Brown University; Rhode Island; USA |
Burroughs Wellcome Career Award at the Scientific Interface ; NHGRI R01 HG5690 |
PMID:22452995 | Free, Available for download, Freely available | OMICS_00317 | http://code.google.com/p/gasv/downloads/list | SCR_005259 | GASVPro: Geometric Analysis of Structural Variants | 2026-08-29 11:22:18 | 8 | ||||
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BioExtract Resource Report Resource Website 10+ mentions |
BioExtract (RRID:SCR_005397) | BioExtract | service resource | An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. | nucleotide sequence, protein sequence, viridiplantae, viridiplantae protein, nucleotide, sequence, protein, viridiplantae, workflow, software, database, bioinformatics, platform, genome, genomic analysis, analytic tool |
is listed by: OMICtools is listed by: SoftCite is related to: NCBI Nucleotide is related to: NCBI Protein Database is related to: UniProt is related to: UniRef is related to: EMBOSS is related to: BioMoby is related to: KEGG has parent organization: Indiana University; Indiana; USA has parent organization: University of South Dakota; South Dakota; USA |
NSF 0090732; NSF IOS-1126481 |
PMID:21546552 PMID:20865520 PMID:20150665 PMID:20054995 |
OMICS_01138 | SCR_005397 | BioExtract Server | 2026-08-29 11:22:25 | 12 | ||||||
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KGGSeq Resource Report Resource Website 50+ mentions |
KGGSeq (RRID:SCR_005311) | KGGSeq | software resource | A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data. | genomic, genetic, sequence, mutation, exome sequencing, disease, gene, variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Monogenic disorder, Cancer | PMID:22241780 | biotools:kggseq, OMICS_02260 | https://bio.tools/kggseq | SCR_005311 | KGGSeq: A biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data | 2026-08-29 11:22:18 | 58 | |||||
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MAKER Web Annotation Service Resource Report Resource Website 1+ mentions |
MAKER Web Annotation Service (RRID:SCR_005318) | MWAS | data access protocol, production service resource, service resource, software resource, web service | The MAKER Web Annotation Service (MWAS) is an easily configurable web-accessible genome annotation pipeline. It''''s purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence (i.e. BAC clones, small whole genomes, preliminary sequencing data, etc.) to independently annotate and analyze their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline MAKER, and users who wish to annotate larger datasets and whole genomes are free to download MAKER for use on their own systems. MWAS identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MWAS can also automatically train popular gene prediction algorithms for use on new genomes for which pre-existing information is limited. MAKER is a member of the Generic Model Organism Database (GMOD) project and output produced by this site can be directly used with other GMOD tools. Annotations can be directly viewed online by the user via GBrowse, JBrowse, and Apollo, or they can be downloaded for local analysis and integration into a genome database. MWAS also supplies summary statistics on sequence features via the Sequence Ontology tool SOBA. MWAS should prove especially useful for emerging model organism genome projects with minimal bioinformatics expertise and computer resources, since a user can produce final genome annotations without having to install and configure any software locally. | data management, human genome map, genome annotation, annotation, curation, genome, sequence |
is related to: MAKER has parent organization: University of Utah; Utah; USA |
nlx_144374 | SCR_005318 | 2026-08-29 11:22:18 | 7 | |||||||||
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FaBox Resource Report Resource Website 100+ mentions |
FaBox (RRID:SCR_005350) | FaBox | software resource | Tools for splitting, joining and otherwise manipulating FASTA format sequence files. The first tools in the toolbox is for manipulating fasta headers, cropping alignments and doing some sequence comparison allowing users to combine the description of data (often in excel spreadsheets) with the actual data (often DNA sequences). Also, producing correct input files for a range of programs seems to be problematic for the average user. Hence, some converters in some of the services have been included as well as some stand-alone converters. The converters are not necessarily meant to provide the final input file, but you''ll get a valid input file for Arlequin, MrBayes etc. - that you may further edit so it suit your needs. This means that you may need to combine several of the tools to finish your handling - but it keeps it relatively simple to use. Please note that FaBox is written in PHP and ONLY RUNS ON A WEBSERVER. | fasta, dna, protein sequence, dna sequence, protein, sequence, php |
is listed by: OMICtools has parent organization: Aarhus University; Aarhus; Denmark |
Acknowledgement requested | OMICS_01165 | SCR_005350 | FaBox - an online fasta sequence toolbox | 2026-08-29 11:22:25 | 120 | |||||||
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PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | data or information resource, data repository, database, service resource, software resource, storage service resource | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | 2026-08-29 11:22:14 | 32 | ||||||
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TIGRFAMS Resource Report Resource Website 100+ mentions |
TIGRFAMS (RRID:SCR_005493) | JCVI TIGRFAMS, TIGRFAM | data or information resource, data set, database | Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site. | sequence alignment, hidden markov model, protein sequence, classification, protein, protein family, sequence homology, sequence, homology, function, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: InterPro is related to: InterPro has parent organization: J. Craig Venter Institute |
PMID:23197656 | Free | nif-0000-03560, OMICS_01700, biotools:tigrfams | https://bio.tools/tigrfams | http://www.tigr.org/TIGRFAMs | SCR_005493 | TIGRFAMs | 2026-08-29 11:22:26 | 142 | ||||
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Bowtie Resource Report Resource Website 10000+ mentions |
Bowtie (RRID:SCR_005476) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software ultrafast memory efficient tool for aligning sequencing reads. Bowtie is short read aligner. | sequence, analysis, long, reference, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: TopHat is used by: BS Seeker is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Bowtie 2 has parent organization: Johns Hopkins University; Maryland; USA is required by: RelocaTE |
Amazon Web Services in Education Research ; NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:19261174 DOI:10.1186/gb-2009-10-3-r25 |
Free, Available for download, Freely available | biotools:bowtie, OMICS_00653 | https://github.com/BenLangmead/bowtie, https://bio.tools/bowtie, https://sources.debian.org/src/bowtie/ | SCR_005476 | 2026-08-29 11:22:16 | 13799 | ||||||
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geneXplain Resource Report Resource Website 50+ mentions |
geneXplain (RRID:SCR_005573) | GeneXplain | data processing software, software application, software resource, software toolkit, workflow software | An online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system. With this system, you can edit the predefined workflows or compose your own workflows from scratch. Your own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses. GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field. | scientific workflow, bioinformatics, systems biology, network modeling, microarray, proteomics, mirna, chip-chip, sequence, biomarker, gene expression | nlx_146199 | SCR_005573 | geneXplain GmbH | 2026-08-29 11:22:27 | 73 | |||||||||
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Chromaseq Resource Report Resource Website 1+ mentions |
Chromaseq (RRID:SCR_005587) | Chromaseq | software resource | A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap. | chromatogram, sequence, mesquite |
is listed by: OMICtools has parent organization: Oregon State University; Oregon; USA |
NSF EF-0531754 | Acknowledgement required | OMICS_01017 | SCR_005587 | Chromaseq: a package for processing chromatograms and sequence data in Mesquite | 2026-08-29 11:22:27 | 7 | ||||||
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IFTI-Mirage Resource Report Resource Website 1+ mentions |
IFTI-Mirage (RRID:SCR_000505) | data or information resource, database, portal | A resource for information pertaining to methodologies, tools and technologies of gene expression. The website offers resources for sequence analysis, database services, and other technologies of gene expression and regulation. | bioinformatics, gene, expression, database, technology, method, tool, sequence, regulation |
is parent organization of: object-oriented Transcription Factors Database is parent organization of: TfSiteScan |
Public, Available to the research community | nlx_19877 | SCR_000505 | Institute for Transcriptional Informatics-Molecular Informatics Resource for the Analysis of Gene Expression, MIRAGE | 2026-08-29 11:28:24 | 5 | ||||||||
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skewer Resource Report Resource Website 10+ mentions |
skewer (RRID:SCR_001151) | skewer | data processing software, software application, software resource | Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences. | illumina, unix/linux, c++, adapter trimming, paired-end, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24925680 | Free, Available for download, Freely available | OMICS_02106, biotools:skewer | https://bio.tools/skewer, https://sources.debian.org/src/skewer/, https://github.com/relipmoc/skewer | SCR_001151 | skewer - A fast and sensitive adapter trimmer for illumina paired-end sequences | 2026-08-29 11:28:32 | 14 |
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