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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BlackOPs Resource Report Resource Website |
BlackOPs (RRID:SCR_000032) | software application, data processing software, data analysis software, software resource, sequence analysis software | Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls. | rna seq, false positive, genome editing, rna editing, mismapped reads | has parent organization: SourceForge | PMID:23935067 | Free, Available for download, Freely available | OMICS_01229 | SCR_000032 | BlackOPs: RNA-Seq Variant Blacklist Tool | 2026-02-17 09:59:23 | 0 | |||||||
|
POPBAM Resource Report Resource Website |
POPBAM (RRID:SCR_000464) | POPBAM | data analysis software, software application, data processing software, software resource | A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome. | next-generation sequencing, evolution, population, bam, genome, evolutionary genetics, c++, short read, sequence alignment, sliding window, command-line, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: University of Rochester; New York; USA |
PMID:24027417 | Free, Available for download, Freely available | biotools:popbam, OMICS_01559 | https://bio.tools/popbam | http://popbam.sourceforge.net/ | SCR_000464 | 2026-02-17 09:59:27 | 0 | |||||
|
BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | software application, data processing software, data analysis software, software resource, data visualization software | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-02-17 09:59:28 | 1 | |||||
|
AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | 2026-02-17 09:59:35 | 0 | |||||||
|
UnoSeq Resource Report Resource Website 1+ mentions |
UnoSeq (RRID:SCR_005116) | UnoSeq | software library, software resource, software toolkit | A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists. | java, expression profile, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20194116 | OMICS_01296 | SCR_005116 | UnoSeq - Expression profiling with next generation sequencing without a reference genome | 2026-02-17 10:00:29 | 1 | |||||||
|
SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | production service resource, analysis service resource, service resource, software resource, data analysis service | 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 | 2026-02-17 10:00:44 | 2 | ||||||
|
PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | storage service resource, data or information resource, database, service resource, software resource, data repository | 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 | 2026-02-17 10:00:52 | 32 | ||||||
|
Maqview Resource Report Resource Website |
Maqview (RRID:SCR_005632) | MaqView | data visualization software, data processing software, software application, software resource | A graphical read alignment viewer specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License | OMICS_00889, biotools:maqview | https://bio.tools/maqview https://sources.debian.org/src/maqview/ |
SCR_005632 | Mapping and Assembly with Qualities Viewer, M.A.Q Viewer | 2026-02-17 10:00:56 | 0 | |||||
|
Biologic Stylus Resource Report Resource Website |
Biologic Stylus (RRID:SCR_002991) | Biologic Stylus | software application, source code, software resource, simulation software | Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python | bioinformatics, simulation | has parent organization: SourceForge | Free, Available for download, Freely available | nif-0000-30198 | SCR_002991 | biologicstylus | 2026-02-17 10:00:07 | 0 | |||||||
|
Hadoop-BAM Resource Report Resource Website 1+ mentions |
Hadoop-BAM (RRID:SCR_005516) | Hadoop-BAM | software library, software resource, software toolkit | A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. | mapreduce/hadoop, java, next generation sequencing data, cloud |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22302568 | MIT License | OMICS_01051 | SCR_005516 | 2026-02-17 10:00:46 | 7 | |||||||
|
Comparative Data Analysis Ontology Resource Report Resource Website |
Comparative Data Analysis Ontology (RRID:SCR_010297) | CDAO | data or information resource, ontology, controlled vocabulary | 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 | 2026-02-17 10:01:41 | 0 | |||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | software application, data processing software, algorithm resource, data analysis software, software resource, sequence analysis software | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo https://sources.debian.org/src/uc-echo/ |
SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-02-17 10:02:05 | 310 | |||||
|
BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | alignment software, software application, data processing software, data analysis software, software resource, sequence analysis software, image analysis software | 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 | 2026-02-17 10:01:53 | 2291 | |||||
|
TagCleaner Resource Report Resource Website 50+ mentions |
TagCleaner (RRID:SCR_011846) | software application, web application, software resource, standalone software | A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets. | tag sequence, standalone software, web application, microbiome, genomic, metagenomic, datasets |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: SourceForge |
Available for download | OMICS_01094 | SCR_011846 | 2026-02-17 10:01:38 | 63 | |||||||||
|
Multivariate Analysis of Transcript Splicing Resource Report Resource Website 100+ mentions |
Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) | MATS | data analysis software, software application, data processing software, software resource | Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. | Differential alternative splicing events, splicing events calculation, RNA-Seq data, gene isoform ratio, alternative splicing patterns, patterns detection, patterns analysis, replicate RNA-Seq data |
is listed by: OMICtools is listed by: SourceForge has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA |
Free, Available for download, Freely available | OMICS_01336, SCR_020941 | SCR_013049 | RNAseq MATS, RMATS, rMATS, MATS, RNA MATS | 2026-02-17 10:02:29 | 192 | |||||||
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Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | software development environment, software development tool, software application, community building portal, data or information resource, software resource, portal | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-02-17 10:02:21 | 24 | ||||
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Dissect Resource Report Resource Website |
Dissect (RRID:SCR_000058) | Dissect | alignment software, software application, data processing software, software resource, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. | Structural events containing transcripts, transcriptome-to-genome alignment, identify and characterize transcriptomic events, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:22689759 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01346, biotools:dissect | https://bio.tools/dissect | SCR_000058 | Dissect: DIScovery of Structural Events Containing Transcripts, DIScovery of Structural Events Containing Transcripts | 2026-02-17 09:59:23 | 0 | |||||
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MUMmerGPU Resource Report Resource Website 1+ mentions |
MUMmerGPU (RRID:SCR_001200) | MUMmerGPU | software application, data processing software, software resource | Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer. | parallel computation 4, high-throughput sequencing, sequence alignment, dna, graphics processing unit |
is listed by: OMICtools is related to: MUMmer has parent organization: SourceForge has parent organization: University of Maryland; Maryland; USA |
NLM R01 LM006845; NIGMS R01 GM083873 |
PMID:20161021 | Free, Available for download, Freely available | OMICS_02151 | SCR_001200 | High-throughput sequence alignment using Graphics Processing Units | 2026-02-17 09:59:36 | 5 | |||||
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skewer Resource Report Resource Website 10+ mentions |
skewer (RRID:SCR_001151) | skewer | software application, data processing software, 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 | 2026-02-17 09:59:36 | 11 | |||||
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SPInDel Resource Report Resource Website 1+ mentions |
SPInDel (RRID:SCR_004509) | SPInDel | data or information resource, data set, software resource | A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species. | virus, indel, dna barcoding, alignment, nucleotide sequence, visualization, conserved region, pcr primer, phylogenetic, variant |
is listed by: OMICtools has parent organization: University of Porto; Porto; Portugal has parent organization: SourceForge |
PMID:22978681 PMID:20923781 |
Acknowledgement requested, Free, Public | OMICS_01496 | SCR_004509 | SPecies Identification by Insertions/Deletions, SPInDel - Species identification by insertions/deletions | 2026-02-17 10:00:33 | 2 |
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