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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Maryland; Maryland; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2026-08-29 11:23:45 | 468 | |||||||
|
Pathema Resource Report Resource Website 1+ mentions |
Pathema (RRID:SCR_010585) | Pathema | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource. | bacillus anthracis, clostridium botulinum, burkholderia mallei, burkholderia pseudomallei, clostridium perfringens, entamoeba histolytica, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: J. Craig Venter Institute |
NIAID contract HHSN266200400038C | PMID:19843611 | biotools:pathema, nlx_45829 | https://bio.tools/pathema | SCR_010585 | Pathema Genome Resource, Pathema Bioinformatics Resource Center | 2026-08-29 11:23:33 | 6 | |||||
|
ABySS Resource Report Resource Website 500+ mentions |
ABySS (RRID:SCR_010709) | ABySS | data analysis software, data processing software, sequence analysis software, software application, software resource | Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements. | paired-end sequence assembler, short reads, assembling human genome, large genomes, bloom filter, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
British Columbia Cancer Foundation ; Genome British Columbia ; Genome Canada ; NHGRI R01HG007182 |
PMID:19251739 DOI:10.1101/068338 DOI:10.1101/gr.214346.116 |
Free, Available for download, Freely available | OMICS_00006, biotools:abyss | https://github.com/bcgsc/abyss, https://sources.debian.org/src/abyss/, https://bio.tools/abyss, | SCR_010709 | ABySS 1.0, ABySS 2.0 | 2026-08-29 11:23:35 | 808 | ||||
|
icy Resource Report Resource Website 100+ mentions |
icy (RRID:SCR_010587) | ICY | data processing software, image analysis software, image processing software, service resource, software application, software development environment, software development tool, software repository, software resource, source code | An open community platform for bioimage informatics providing the software resources to visualize, annotate and quantify bioimaging data. To bridge the gap between developers and users, it combines: a) an open-source image analysis software, offering a powerful and flexible environment for developers such as applied mathematicians to write algorithms fast and efficiently; b) a common set of tools to view and manipulate data, and a set of plugins to perform specific quantification or analysis on images; c) a community-based website centralizing all plugins and resources to facilitate their management and maximize their visibility towards users. Workspaces are virtual groups of plugins dedicated to a specific application or image processing domain. By downloading a workspace, ICY automatically installs all corresponding plugins. The workspaces are enabled, but the editing section is not ready yet. If you want to publish a plugin on this website, its code has to be GPL. Source code is available and provided in each application download. | image analysis, microscopy, javascript, python, plugin, protocol, script, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Pasteur Institute |
Centre National de la Recherche Scientifique ; French National Research Agency ANR-10-INBS-04-06 |
PMID:22743774 | Free, Open unspecified license, GNU General Public License, v3, The community can contribute to this resource | biotools:icy, nlx_45928 | https://bio.tools/icy | SCR_010587 | icy bioimage analysis | 2026-08-29 11:23:49 | 355 | ||||
|
Geneious Resource Report Resource Website 10000+ mentions |
Geneious (RRID:SCR_010519) | data analysis software, data management software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools. | Sequence alignment software, data management software, analysis software, Geneious Biologics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is parent organization of: Geneious Microsatellite Plugin |
PMID:22543367 | Restricted | OMICS_00016, biotools:geneious | http://nebc.nerc.ac.uk/news/geneiousonbl, https://bio.tools/geneious | SCR_010519 | Geneious Prime, Geneious 11.0, Geneious 11.1.2, Geneious 8.1, Geneious Basic | 2026-08-29 11:23:43 | 13589 | ||||||
|
CNVer Resource Report Resource Website 1+ mentions |
CNVer (RRID:SCR_010820) | CNVer | software resource | A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:cnver, OMICS_00341 | https://bio.tools/cnver | SCR_010820 | 2026-08-29 11:23:55 | 8 | ||||||||
|
Relate Resource Report Resource Website 10+ mentions |
Relate (RRID:SCR_010794) | Relate | software resource | Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:19025785 | biotools:relateadmix, OMICS_00207 | https://bio.tools/relateadmix | SCR_010794 | 2026-08-29 11:23:37 | 47 | |||||||
|
MoDIL Resource Report Resource Website 1+ mentions |
MoDIL (RRID:SCR_010764) | MoDIL | software resource | Software for a novel method for finding medium sized indels from high throughput sequencing datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
OMICS_00066, biotools:modil | https://bio.tools/modil | SCR_010764 | MoDIL: Detecting INDEL Variation with Clone-end Sequencing | 2026-08-29 11:23:36 | 4 | |||||||
|
MISA Resource Report Resource Website 1000+ mentions |
MISA (RRID:SCR_010765) | MISA | software resource | Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00110, biotools:misa | https://bio.tools/misa | SCR_010765 | MISA - MIcroSAtellite identification tool | 2026-08-29 11:23:53 | 1053 | |||||||
|
GensearchNGS Resource Report Resource Website 10+ mentions |
GensearchNGS (RRID:SCR_010802) | GensearchNGS | software resource | An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Commercial license | OMICS_00287, biotools:gensearchngs | https://bio.tools/gensearchngs | SCR_010802 | 2026-08-29 11:23:46 | 23 | |||||||
|
HomSI Resource Report Resource Website 1+ mentions |
HomSI (RRID:SCR_010771) | HomSI | software resource | A software tool that identifies homozygous regions using deep sequence data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24307702 | Free | OMICS_00124, biotools:homsi | https://bio.tools/homsi | SCR_010771 | Homozygous Stretch Identifier from next-generation sequencing data, HomSI - Homozygous Stretch Identifier from next-generation sequencing data | 2026-08-29 11:23:53 | 4 | |||||
|
CONTRA Resource Report Resource Website 100+ mentions |
CONTRA (RRID:SCR_010814) | CONTRA | software resource | A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00331, biotools:contra | https://bio.tools/contra | SCR_010814 | 2026-08-29 11:23:55 | 291 | ||||||||
|
breseq Resource Report Resource Website 100+ mentions |
breseq (RRID:SCR_010810) | breseq | software resource | A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes. | windows, genomics, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
OMICS_00298, biotools:breseq | https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing, https://bio.tools/breseq | SCR_010810 | breseq - Determine mutations in evolved microbes from next-generation sequencing data | 2026-08-29 11:23:38 | 474 | |||||||
|
MutPred Resource Report Resource Website 100+ mentions |
MutPred (RRID:SCR_010778) | MutPred | software resource, web application | Web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. | bio.tools |
is used by: HmtVar is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
biotools:mutpred, OMICS_00154 | https://bio.tools/mutpred | SCR_010778 | 2026-08-29 11:23:37 | 470 | ||||||||
|
MutSig Resource Report Resource Website 100+ mentions |
MutSig (RRID:SCR_010779) | MutSig | software resource | Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:23770567 | OMICS_00155, biotools:MutSig2CV | https://bio.tools/MutSig2CV | SCR_010779 | Mutation Significance | 2026-08-29 11:23:53 | 129 | ||||||
|
SVDetect Resource Report Resource Website 10+ mentions |
SVDetect (RRID:SCR_010812) | SVDetect | software resource | Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads. | structural variation, sequencing, chromosomal rearrangement, high-throughput sequencing, solid, illumina, genome, insertion, deletion, inversion, duplication, translocation, command-line, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Curie Institute; Paris; France |
PMID:20639544 | GNU General Public License, v3 | OMICS_00324, biotools:svdetect | https://bio.tools/svdetect | SCR_010812 | SVDetect: a tool to detect genomic structural variations from paired-end and mate-pair sequencing data | 2026-08-29 11:23:46 | 24 | |||||
|
nsSNPAnalyzer Resource Report Resource Website 50+ mentions |
nsSNPAnalyzer (RRID:SCR_010780) | nsSNPAnalyzer | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
OMICS_00156, biotools:nssnpanalyzer | https://bio.tools/nssnpanalyzer | SCR_010780 | nsSNPAnalyzer: predicting disease-associated nonsynonymous single nucleotide polymorphisms | 2026-08-29 11:23:46 | 50 | |||||||
|
ALLPATHS-LG Resource Report Resource Website 100+ mentions |
ALLPATHS-LG (RRID:SCR_010742) | ALLPATHS-LG | software resource | Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. | genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:21187386 | OMICS_00007, biotools:allpaths-lg | https://bio.tools/allpaths-lg | SCR_010742 | 2026-08-29 11:23:52 | 237 | |||||||
|
SOAPdenovo Resource Report Resource Website 1000+ mentions |
SOAPdenovo (RRID:SCR_010752) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, rna, dna, de novo, genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20019144 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00031, biotools:soapdenovo, SCR_014986 | https://github.com/aquaskyline/SOAPdenovo2, https://bio.tools/soapdenovo, https://sources.debian.org/src/soapdenovo/, | SCR_010752 | SOAPdenovo2 | 2026-08-29 11:23:36 | 1342 | ||||||
|
Velvet Resource Report Resource Website 1000+ mentions |
Velvet (RRID:SCR_010755) | Velvet | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | de novo, genomic, assembly, short, read, sequencing, de Bruijn, graph, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Velvet-SC is related to: shovill has parent organization: European Bioinformatics Institute |
EMBL | PMID:18349386 DOI:10.1101/gr.074492.107 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00038, biotools:velvet | https://www.ebi.ac.uk/~zerbino/velvet/, https://bio.tools/velvet, https://sources.debian.org/src/velvet/ | SCR_010755 | 2026-08-29 11:23:36 | 1039 |
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