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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PerM Resource Report Resource Website 50+ mentions |
PerM (RRID:SCR_004223) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. | Short sequencing mapping, short sequencing read, next-generation sequencing, genome, alignment, short read, abi, solid, illumina, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clippers has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 DOI:10.1093/bioinformatics/btp486 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00675, biotools:perm | https://bio.tools/perm, https://sources.debian.org/src/perm/ | SCR_004223 | PERiodic seed Mapping, Periodic seed Mapping | 2026-09-12 12:56:10 | 60 | ||||||
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NEXTDB Resource Report Resource Website 10+ mentions |
NEXTDB (RRID:SCR_004480) | NextDB | analysis service resource, atlas, data analysis service, data or information resource, database, expression atlas, production service resource, service resource | Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae | rnai phenotype, homology, blast, fasta, chromosome map, cosmid, gene, cdna clone, genome, in situ hybridization, expressed sequence tag, developmental stage, sequence, embryonic caenorhabditis elegans, chromosome, phenotype, blastx, clone, sequence tag, yac, predicted gene, protein, development, larval caenorhabditis elegans, image collection, experimental protocol, FASEB list |
is related to: Expression Patterns for C. elegans promoter GFP fusions is related to: Expression Patterns for C. elegans promoter GFP fusions has parent organization: National Institute of Genetics; Shizuoka; Japan |
Core Research for Evolutional Science and Technology ; Japan Science and Technology Corporation ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
Permission required, Acknowledgement required | nlx_46406 | SCR_004480 | Nematode Expression Pattern DataBase | 2026-09-12 12:56:13 | 35 | ||||||
|
ACT: Artemis Comparison Tool Resource Report Resource Website 10+ mentions |
ACT: Artemis Comparison Tool (RRID:SCR_004507) | ACT | software resource | A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | dna sequence, genome, synteny, pairwise comparison |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | PMID:15976072 | GNU General Public License | OMICS_00928, nlx_48986 | SCR_004507 | Artemis Comparison Tool | 2026-09-12 12:56:13 | 47 | |||||
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Stem Cell Commons Resource Report Resource Website 1+ mentions |
Stem Cell Commons (RRID:SCR_004415) | Stem Cell Commons | analysis service resource, data or information resource, data repository, data set, database, production service resource, service resource, software resource, source code, storage service resource | Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. | therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model |
is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard Stem Cell Institute |
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. | PMID:24303302 | Open unspecified license | nlx_42085 | http://bloodprogram.hsci.harvard.edu/ | SCR_004415 | HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program | 2026-09-12 12:56:12 | 2 | ||||
|
deStruct Resource Report Resource Website 1+ mentions |
deStruct (RRID:SCR_004747) | deStruct | software resource | A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing. | structural variation, genome, genomics |
is listed by: OMICtools has parent organization: Google Code |
Tumor, Cancer | Open unspecified license | OMICS_00314 | SCR_004747 | deStruct - Bioinformatics tool for identifying structural variation in tumour genomes | 2026-09-12 12:56:16 | 8 | ||||||
|
VariationHunter Resource Report Resource Website 10+ mentions |
VariationHunter (RRID:SCR_004865) | VariationHunter | software resource | A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. | structural variation, genome, next-generation sequencing |
is listed by: OMICtools is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:22048523 PMID:20529927 |
OMICS_00328 | SCR_004865 | VariationHunter-CommonLaw | 2026-09-12 12:56:17 | 12 | |||||||
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Phymm and PhymmBL Resource Report Resource Website 10+ mentions |
Phymm and PhymmBL (RRID:SCR_004751) | Phymm, PhymmBL | software resource | Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. | metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short read |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM R01-LM006845 | PMID:19648916 PMID:21527926 |
Open-source license | OMICS_01461 | SCR_004751 | 2026-09-12 12:56:16 | 12 | ||||||
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GeneDB Tbrucei Resource Report Resource Website 10+ mentions |
GeneDB Tbrucei (RRID:SCR_004786) | GeneDB_Tbrucei, GeneDB Tbrucei, GeneDB T. brucei | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of the most recent sequence updates and annotations for the T. brucei genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. T. brucei possesses a two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split into three classes of chromosomes according to their size on pulsed-field gel electrophoresis, 11 pairs of megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and minichromosomes (50-100 kb). The T. brucei genome contains a ~0.5Mb segmental duplication affecting chromosomes 4 and 8, which is responsible for some 75 gene duplicates unique to this species. A comparative chromosome map of the duplicons can be accessed here (PubmedID 18036214). Protozoan parasites within the species Trypanosoma brucei are the etiological agent of human sleeping sickness and Nagana in animals. Infections are limited to patches of sub-Saharan Africa where insects vectors of the Glossina genus are endemic. The most recent estimates indicate between 50,000 - 70,000 human cases currently exist, with 17 000 new cases each year (WHO Factsheet, 2006). In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries. | blast, sequence, annotation, genome |
is used by: NIF Data Federation is related to: AmiGO is related to: TriTrypDB has parent organization: GeneDB |
Wellcome Trust | PMID:16020726 | nlx_78417 | SCR_004786 | Trypanosoma brucei TREU927 homepage on GeneDB, Trypanosoma brucei TREU927 on GeneDB | 2026-09-12 12:56:16 | 17 | ||||||
|
SSPACE Resource Report Resource Website 100+ mentions |
SSPACE (RRID:SCR_005056) | SSPACE | software resource | A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. | scaffolding, contig, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21149342 DOI:10.1093/bioinformatics/btq683 |
GNU General Public License, Registration required | biotools:sspace, OMICS_00050 | https://bio.tools/sspace, https://sources.debian.org/src/sspace/ | SCR_005056 | 2026-09-12 12:56:20 | 435 | ||||||
|
AGORA Resource Report Resource Website 100+ mentions |
AGORA (RRID:SCR_005070) | AGORA | software resource | An algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. AGORA takes as input two data structures: OpMap ? an ordered list of fragment sizes representing the optical map; and Edges ? a list of de Bruijn graph edges with their corresponding sequences. | genome assembly, genome, reconstruction | is listed by: OMICtools | PMID:22856673 | OMICS_00039 | SCR_005070 | Assembly Guided by Optical Restriction Alignment | 2026-09-12 12:56:20 | 105 | |||||||
|
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 | 2026-09-12 12:56:21 | 46 | |||||||
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VirusFinder Resource Report Resource Website 10+ mentions |
VirusFinder (RRID:SCR_005205) | VirusFinder | software resource | Software tool for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. Specifically, it detects virus infection, co-infection with multiple viruses, virus integration sites in host genomes, as well as mutations in the virus genomes. It also facilitates virus discovery by reporting novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. VirusFinder 2 works with both paired-end and single-end data, unlike the previous 1.x versions that accepted only paired-end reads. The types of NGS data that VirusFinder 2 can deal with include whole genome sequencing (WGS), whole transcriptome sequencing (RNA-Seq), targeted sequencing data such as whole exome sequencing (WES) and ultra-deep amplicon sequencing. | next-generation sequencing, virus, integration site, genome, mutation, virus genome, contig, paired-end, single-end, whole genome sequencing, whole transcriptome sequencing, rna-seq, targeted sequencing, whole exome sequencing, ultra-deep amplicon sequencing |
is listed by: OMICtools has parent organization: Vanderbilt University; Tennessee; USA |
Viral infection | PMID:23717618 | OMICS_00226 | SCR_005205 | 2026-09-12 12:56:22 | 16 | |||||||
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Genomic Datasharing Resource Report Resource Website 1+ mentions |
Genomic Datasharing (RRID:SCR_005233) | GDS | data or information resource, feed, listserv, narrative resource, standard specification | NIH established expectations for sharing data obtained through NIH-funded genome-wide association studies (GWAS) with the implementation of the GWAS Policy. Information and resources related to the GWAS Policy can be found on this website. | genome-wide association study, genome, data sharing |
is listed by: OMICtools has parent organization: National Institutes of Health |
NIH | OMICS_00272 | SCR_005233 | GWAS, Genome-Wide Association Studies | 2026-09-12 12:56:23 | 5 | |||||||
|
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 | 2026-09-12 12:56:22 | 2 | ||||||
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NGS-SNP Resource Report Resource Website 10+ mentions |
NGS-SNP (RRID:SCR_005182) | NGS-SNP | software resource | A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species. | annotation, snp, sequencing, transcript, genome, reference sequence, indel, annotate, reference chromosome, reference transcript, gene, command-line |
is listed by: OMICtools is related to: Ensembl has parent organization: University of Alberta; Alberta; Canada |
OMICS_00177 | SCR_005182 | 2026-09-12 12:56:22 | 33 | |||||||||
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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 | 2026-09-12 12:56:23 | 8 | ||||
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PRISM (Stanford database) Resource Report Resource Website 10000+ mentions |
PRISM (Stanford database) (RRID:SCR_005375) | PRISM | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomic, transcription factor, function, transcription factor binding site, transcription factor regulator, biological role, target gene, target genomic region, genome, FASEB list |
is listed by: OMICtools is listed by: SoftCite is related to: GREAT: Genomic Regions Enrichment of Annotations Tool has parent organization: Stanford University School of Medicine; California; USA |
PMID:23382538 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00489 | SCR_005375 | Predicting Regulatory Information from Single Motifs | 2026-09-12 12:56:25 | 40822 | ||||||
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Ergatis Resource Report Resource Website 1+ mentions |
Ergatis (RRID:SCR_005377) | Ergatis | software resource | A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level. | workflow, bioinformatics, workflow management, pipeline, computation, genomics, genome, processing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Maryland School of Medicine; Maryland; USA |
PMID:20413634 | Artistic License | OMICS_01140 | SCR_005377 | ergatis: workflow creation and monitoring interface | 2026-09-12 12:56:25 | 2 | ||||||
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CREST Resource Report Resource Website 50+ mentions |
CREST (RRID:SCR_005257) | CREST | software resource | An algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. CREST uses pieces of DNA called soft clips to find structural variations. Soft clips are the DNA segments produced during sequencing that fail to properly align to the reference genome as the sample genome is reassembled. CREST uses the soft clips to precisely identify sites of chromosomal rearrangement or where pieces of DNA are inserted or deleted. | genome, structural variation, next-generation sequencing, soft clip |
is listed by: OMICtools has parent organization: Pennsylvania State University |
PMID:21666668 | OMICS_00312 | SCR_005257 | 2026-09-12 12:56:23 | 57 | ||||||||
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MolBioLib Resource Report Resource Website |
MolBioLib (RRID:SCR_005372) | MolBioLib | software resource | A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++. | c++, next-generation sequencing, genomic, analysis, genome |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815363 | OMICS_01145 | SCR_005372 | MolBioLib: C++11 framework for rapid develop and deploy of bioinformatic tasks | 2026-09-12 12:56:25 | 0 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
