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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Taipan Resource Report Resource Website 1+ mentions |
Taipan (RRID:SCR_007330) | Taipan | software resource | A fast hybrid short-read assembly tool. | c, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19535537 | GNU General Public License, v2 | OMICS_00035, biotools:taipan | https://bio.tools/taipan | SCR_007330 | 2026-09-05 06:26:10 | 2 | ||||||
|
GenoTan Resource Report Resource Website 1+ mentions |
GenoTan (RRID:SCR_007935) | GenoTan | software resource | A free software tool to identify length variation of microsatellites from short sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24135263 | GNU General Public License, v3 | biotools:genotan | https://bio.tools/genotan | SCR_007935 | GenoTan - Genotyping of microsatellite loci | 2026-09-05 06:26:15 | 1 | |||||
|
BRIG Resource Report Resource Website 500+ mentions |
BRIG (RRID:SCR_007802) | BRIG | software resource | A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.1186/1471-2164-12-402 | OMICS_00929, biotools:brig | https://bio.tools/brig, https://sources.debian.org/src/brig/ | SCR_007802 | BLAST Ring Image Generator | 2026-09-05 06:26:15 | 561 | ||||||
|
SeqPig Resource Report Resource Website 1+ mentions |
SeqPig (RRID:SCR_008548) | SeqPig | software resource | A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters. | mapreduce/hadoop |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24149054 | OMICS_01226 | SCR_008548 | 2026-09-05 06:26:24 | 2 | ||||||||
|
Gecko Resource Report Resource Website 500+ mentions |
Gecko (RRID:SCR_009001) | Gecko | software resource | A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15588317 | OMICS_00758 | SCR_009001 | Gene Expression: Computation and Knowledge Organization, Geckoe | 2026-09-05 06:26:31 | 547 | ||||||||
|
SCALCE Resource Report Resource Website |
SCALCE (RRID:SCR_009658) | SCALCE | software resource | A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00969 | SCR_009658 | Boosting Sequence Compression Algorithms using Locally Consistent Encoding | 2026-09-05 06:26:36 | 0 | |||||||||
|
Comparative Data Analysis Ontology Resource Report Resource Website |
Comparative Data Analysis Ontology (RRID:SCR_010297) | CDAO | controlled vocabulary, data or information resource, ontology | A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science | owl, biology, evolution, computer science, comparative analysis, phylogenetic tree, operational taxonomic unit, compared character, molecular |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge |
Public domain | nlx_157371 | http://purl.bioontology.org/ontology/CDAO, http://purl.obolibrary.org/obo/cdao.owl | SCR_010297 | 2026-09-05 06:26:38 | 0 | |||||||
|
vipR Resource Report Resource Website 50+ mentions |
vipR (RRID:SCR_010685) | vipR | software resource | A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00081 | SCR_010685 | 2026-09-05 06:26:44 | 60 | ||||||||||
|
FindPeaks Resource Report Resource Website 100+ mentions |
FindPeaks (RRID:SCR_010857) | FindPeaks | software resource | Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis). | chip-seq |
is listed by: OMICtools has parent organization: SourceForge |
BC Cancer Agency ; Michael Smith Foundation for Health Research |
OMICS_00440 | SCR_010857 | 2026-09-05 06:26:48 | 348 | ||||||||
|
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 | 2026-09-05 06:26:47 | 291 | ||||||||
|
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 | 2026-09-05 06:26:47 | 24 | |||||
|
Celera assembler Resource Report Resource Website 50+ mentions |
Celera assembler (RRID:SCR_010750) | Celera assembler | software resource | A de novo whole-genome shotgun (WGS) DNA sequence assembler. |
is listed by: OMICtools is related to: Canu has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00009 | SCR_010750 | 2026-09-05 06:26:45 | 59 | |||||||||
|
DNPTrapper Resource Report Resource Website |
DNPTrapper (RRID:SCR_010981) | DNPTrapper | software resource | An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:16549006 | OMICS_00881 | SCR_010981 | 2026-09-05 06:26:51 | 0 | ||||||||
|
Genovar Resource Report Resource Website 1+ mentions |
Genovar (RRID:SCR_010930) | Genovar | software resource | A Detection and Visualization software tool for Genomic Variants. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Korea National Institute of Health |
Free, Public | OMICS_00724, biottools:genovar | https://bio.tools/genovar | SCR_010930 | 2026-09-05 06:26:50 | 1 | |||||||
|
Hawkeye Resource Report Resource Website 1+ mentions |
Hawkeye (RRID:SCR_010982) | Hawkeye | software resource | A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00884 | SCR_010982 | 2026-09-05 06:26:51 | 9 | ||||||||||
|
PeakRanger Resource Report Resource Website 10+ mentions |
PeakRanger (RRID:SCR_010863) | PeakRanger | software resource | Software for a multi-purpose ChIP Seq peak caller. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21554709 | OMICS_00451, biotools:peakranger | https://bio.tools/peakranger | SCR_010863 | 2026-09-05 06:26:48 | 21 | |||||||
|
SEAL Resource Report Resource Website 100+ mentions |
SEAL (RRID:SCR_010914) | SEAL | software resource | A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21697132 | biotools:seal, OMICS_00682 | https://bio.tools/seal | SCR_010914 | 2026-09-05 06:26:50 | 121 | |||||||
|
BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp. | sequence, alignment, reference, genome, human, short, long, read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill is related to: Proovread is related to: BWA-MEM2 has parent organization: SourceForge is required by: RelocaTE |
PMID:19451168 PMID:20080505 DOI:10.1093/bioinformatics/btp324 |
Free, Available for download, Freely available | SCR_015853, biotools:bwa-sw, OMICS_00654 | https://sourceforge.net/projects/bio-bwa/files/, https://bio.tools/bwa-sw, https://sources.debian.org/src/bwa/ | SCR_010910 | Burrows-Wheeler Aligner (BWA), Burrows-Wheeler Aligner | 2026-09-05 06:26:50 | 2638 | |||||
|
CloudBurst Resource Report Resource Website |
CloudBurst (RRID:SCR_010911) | CloudBurst | software resource | A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19357099 | Free | OMICS_00657, biotools:cloudburst | https://bio.tools/cloudburst | SCR_010911 | 2026-09-05 06:26:50 | 0 | ||||||
|
ERNE Resource Report Resource Website 10+ mentions |
ERNE (RRID:SCR_010912) | ERNE | software resource | A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00662 | SCR_010912 | 2026-09-05 06:26:50 | 48 |
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