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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Mugsy Resource Report Resource Website 50+ mentions |
Mugsy (RRID:SCR_001414) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy. | software, genome, genome alignment, segmentation, pairwise alignment, sequence analysis software |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:21148543 DOI:10.1093/bioinformatics/btq665 |
Free, Available for download, Freely available | OMICS_03606 | https://sources.debian.org/src/mugsy/ | SCR_001414 | SciCrunch Registry | 2026-10-31 12:12:51 | 75 | |||||||
|
MS-Spectre Resource Report Resource Website 1+ mentions |
MS-Spectre (RRID:SCR_000266) | software resource | Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02496 | SCR_000266 | SciCrunch Registry | Mass Spectrometry Analysis Software | 2026-10-31 12:12:36 | 2 | ||||||||
|
BLASTPLOT Resource Report Resource Website |
BLASTPLOT (RRID:SCR_000162) | BLASTPLOT | software resource | A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set. | perl, blast, short sequence, primer, png, png graph |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24685334 | Free, Available for download, Freely available | OMICS_01433 | SCR_000162 | SciCrunch Registry | 2026-10-31 12:12:34 | 0 | |||||||
|
GemSIM Resource Report Resource Website |
GemSIM (RRID:SCR_000167) | GemSIM | software resource | A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface. | bioinformatics, simulation, sequencing, dna, rna, empirical models, Python, command-line, user interface, metagenomic, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge is required by: Wessim |
PMID:22336055 DOI:10.1186/1471-2164-13-74 |
Free, Available for download, Freely available | OMICS_01507, biotools:GemSIM | https://bio.tools/GemSIM | SCR_000167 | SciCrunch Registry | 2026-10-31 12:12:34 | 0 | ||||||
|
GMATo Resource Report Resource Website 1+ mentions |
GMATo (RRID:SCR_000165) | data analysis software, data processing software, sequence analysis software, software application, software resource | A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable. | simple sequence repeat, ssr, microsatellite, genomic, marker design, sequence analysis software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23861572 | Free, Available for download, Freely available | OMICS_00106 | SCR_000165 | SciCrunch Registry | Genome-wide Microsatellite Analyzing Tool, Genome Microsatellite Analyzing Tool, Genome-wide Microsatellite Analyzing Tool (GMATo) | 2026-10-31 12:12:34 | 1 | |||||||
|
ProteinProphet Resource Report Resource Website 10+ mentions |
ProteinProphet (RRID:SCR_000286) | software resource | Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:14632076 | OMICS_02521, biotools:proteinprophet | https://bio.tools/proteinprophet | SCR_000286 | SciCrunch Registry | 2026-10-31 12:12:36 | 11 | ||||||||
|
riboPicker Resource Report Resource Website 1+ mentions |
riboPicker (RRID:SCR_000360) | software resource | Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22155869 | Free, Available for download, Freely available | OMICS_02618, biotools:ribopicker | https://bio.tools/ribopicker | SCR_000360 | SciCrunch Registry | 2026-10-31 12:12:37 | 2 | |||||||
|
ParseCNV Resource Report Resource Website 1+ mentions |
ParseCNV (RRID:SCR_000355) | software resource | Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23293001 | Free, Available for download, Freely available | OMICS_02566 | SCR_000355 | SciCrunch Registry | 2026-10-31 12:12:37 | 1 | ||||||||
|
Kinannote Resource Report Resource Website 1+ mentions |
Kinannote (RRID:SCR_000352) | software resource | Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23904509 | Free, Available for download, Freely available | OMICS_05965 | SCR_000352 | SciCrunch Registry | 2026-10-31 12:12:37 | 2 | ||||||||
|
Jnomics Resource Report Resource Website |
Jnomics (RRID:SCR_000348) | software resource | A collection of cloud-scale DNA sequence analysis tools. | mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_04074 | SCR_000348 | SciCrunch Registry | 2026-10-31 12:12:37 | 0 | |||||||||
|
fqzcomp Resource Report Resource Website 1+ mentions |
fqzcomp (RRID:SCR_000299) | fqzcomp | software resource | A basic fastq compressor, designed primarily for high performance. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00957 | SCR_000299 | SciCrunch Registry | 2026-10-31 12:12:36 | 1 | |||||||
|
BioLemmatizer Resource Report Resource Website 1+ mentions |
BioLemmatizer (RRID:SCR_000117) | software resource | A domain-specific lemmatization software tool for the morphological analysis of biomedical literature. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22464129 | Free, Available for download, Freely available | OMICS_04827 | https://sourceforge.net/projects/biolemmatizer/ | SCR_000117 | SciCrunch Registry | 2026-10-31 12:12:34 | 2 | |||||||
|
SOAPfuse Resource Report Resource Website 1+ mentions |
SOAPfuse (RRID:SCR_000078) | SOAPfuse | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences . | software, resource, open license, DNA sequencing, genome, transcripts, RNA, oligonucleotide |
is listed by: OMICtools is listed by: SourceForge is listed by: SOAP |
PMID:23409703 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01357 | SCR_000078 | SciCrunch Registry | 2026-10-31 12:12:33 | 7 | |||||||
|
Sequence Read Format Resource Report Resource Website 1+ mentions |
Sequence Read Format (RRID:SCR_000132) | SRF | data or information resource, interchange format, narrative resource, standard specification | A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology. | dna sequence, dna sequencing, interchange format |
is listed by: OMICtools has parent organization: SourceForge |
Public, A C++ implementation of Sequence Read Format is available | OMICS_05130 | SCR_000132 | SciCrunch Registry | Sequence Read Format (SRF) | 2026-10-31 12:12:34 | 1 | |||||||
|
exomeSuite Resource Report Resource Website |
exomeSuite (RRID:SCR_000129) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease. | standalone software, c, matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24603341 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04839 | SCR_000129 | SciCrunch Registry | 2026-10-31 12:12:34 | 0 | ||||||||
|
CG-Pipeline Resource Report Resource Website |
CG-Pipeline (RRID:SCR_000047) | software resource | A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly. | perl | has parent organization: SourceForge | PMID:20519285 | Free, Available for download, Freely available | OMICS_04062 | http://sourceforge.net/projects/cg-pipeline/ | SCR_000047 | SciCrunch Registry | 2026-10-31 12:12:32 | 0 | |||||||
|
BlackOPs Resource Report Resource Website |
BlackOPs (RRID:SCR_000032) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | SciCrunch Registry | BlackOPs: RNA-Seq Variant Blacklist Tool | 2026-10-31 12:12:32 | 0 | |||||||
|
Batman-Seq Resource Report Resource Website |
Batman-Seq (RRID:SCR_000048) | Batman-Seq | software resource | A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment. | c++ | is hosted by: SourceForge | Free, Available for download, Freely available | OMICS_00651 | SCR_000048 | SciCrunch Registry | Basic Alignment Tool for MAny Nucleotides | 2026-10-31 12:12:32 | 0 | |||||||
|
HLASeq Resource Report Resource Website |
HLASeq (RRID:SCR_004185) | HLASeq | software resource | An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data. | genotyping, hla, next generation sequencing, gene, command-line, python |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01543 | SCR_004185 | SciCrunch Registry | 2026-10-31 12:13:48 | 0 | ||||||||
|
Vanator Resource Report Resource Website 1+ mentions |
Vanator (RRID:SCR_004370) | Vanator | software resource | A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples. | perl, metagenomic, illumina, alignment, assembly, analysis, profile, virus, clinical, environment, next-generation sequencing, taxonomy, read |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Glasgow; Glasgow; United Kingdom |
PMID:23296970 | OMICS_01505 | SCR_004370 | SciCrunch Registry | Vanator-CVR, Vanator-CVR - A metagenomics & virus discovery pipeline, Virus Alignment de Novo Assembly and Taxonomy On Reads, Vanator-CVR: A metagenomics and virus discovery pipeline | 2026-10-31 12:13:49 | 2 |
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