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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
palfinder Resource Report Resource Website 1+ mentions |
palfinder (RRID:SCR_013174) | palfinder | software resource | A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads. | pacific biosciences |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00111 | SCR_013174 | 2026-09-12 12:57:59 | 6 | |||||||||
|
sam comp Resource Report Resource Website |
sam comp (RRID:SCR_013179) | sam_comp | software resource | A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | OMICS_00968 | SCR_013179 | 2026-09-12 12:57:59 | 0 | ||||||||
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | heurAA - NGS multiplexed amplicon aligner | 2026-09-12 12:58:00 | 0 | ||||||
|
bisReadMapper Resource Report Resource Website |
bisReadMapper (RRID:SCR_013171) | bisReadMapper | software resource | Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00576 | SCR_013171 | bisReadMapper - Software for dealing with DNA methylation sequencing data | 2026-09-12 12:57:59 | 0 | ||||||||
|
SeqTRACS Resource Report Resource Website |
SeqTRACS (RRID:SCR_013294) | SeqTRACS | software resource | Software for a Laboratory Information Management System (LIMS) for tracking, organizing, and accessing sequencing requests and ABI trace files produced by a centralized sequencing core facility. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01013 | SCR_013294 | SeqTRACS: LIMS for sequencing core facilities | 2026-09-12 12:58:01 | 0 | |||||||
|
SOCS Resource Report Resource Website 50+ mentions |
SOCS (RRID:SCR_013223) | SOCS | software resource | Performs ungapped alignment of SOLiD (color space) sequencing reads against reference sequences. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00590 | SCR_013223 | 2026-09-12 12:58:00 | 91 | ||||||||||
|
DSP Resource Report Resource Website |
DSP (RRID:SCR_013114) | DSP | software resource | Pipeline for small genome assembly using SOLiD sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
Apache License, v2 | OMICS_00013 | SCR_013114 | denovo_solid_pipeline | 2026-09-12 12:57:59 | 0 | ||||||||
|
Tuxedo Resource Report Resource Website 100+ mentions |
Tuxedo (RRID:SCR_013194) | Tuxedo | software resource | Software that manages the RNA-sequencing pipeline based on the TopHat suite of software automatically. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01415 | SCR_013194 | Tuxedo: Automated RNA-sequencing Pipeline Script | 2026-09-12 12:58:00 | 103 | |||||||||
|
Crossbow Resource Report Resource Website 1+ mentions |
Crossbow (RRID:SCR_013306) | Crossbow | software resource | A scalable software pipeline for whole genome resequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19930550 DOI:10.1186/gb-2009-10-11-r134 |
biotools:crossbow, OMICS_00284 | https://bio.tools/crossbow | https://sources.debian.org/src/crossbow/ | SCR_013306 | 2026-09-12 12:58:01 | 5 | ||||||
|
EBARDenovo Resource Report Resource Website 1+ mentions |
EBARDenovo (RRID:SCR_011890) | EBARDenovo | software resource | Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01317 | SCR_011890 | 2026-09-12 12:57:41 | 2 | ||||||||||
|
SeqGene Resource Report Resource Website 1+ mentions |
SeqGene (RRID:SCR_011861) | SeqGene | software resource | An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc. |
is listed by: OMICtools has parent organization: SourceForge |
Open unspecified license | OMICS_01134 | SCR_011861 | 2026-09-12 12:57:41 | 2 | |||||||||
|
naiveBayesCall Resource Report Resource Website |
naiveBayesCall (RRID:SCR_011866) | naiveBayesCall | software resource | An efficient model-based base-calling algorithm for high-throughput sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01152, biotools:bayescall | https://bio.tools/bayescall | SCR_011866 | 2026-09-12 12:57:41 | 0 | ||||||||
|
Scalpel Resource Report Resource Website 50+ mentions |
Scalpel (RRID:SCR_012107) | software resource | A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). | software package, c++, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25128977 | biotools:scalpel, OMICS_05395 | https://bio.tools/scalpel | SCR_012107 | 2026-09-12 12:57:45 | 62 | ||||||||
|
MToolBox Resource Report Resource Website 50+ mentions |
MToolBox (RRID:SCR_012112) | software resource | Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25028726 | GNU General Public License | OMICS_05466, biotools:mtoolbox | https://bio.tools/mtoolbox | SCR_012112 | 2026-09-12 12:57:45 | 57 | |||||||
|
ReviSTER Resource Report Resource Website |
ReviSTER (RRID:SCR_012113) | software resource | Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23677944 | GNU General Public License | OMICS_05468 | SCR_012113 | Revise Simple Tandem repeat Error Reads | 2026-09-12 12:57:45 | 0 | |||||||
|
SNP ratio test Resource Report Resource Website 1+ mentions |
SNP ratio test (RRID:SCR_012070) | software resource | Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19620097 | GNU General Public License | biotools:snp_ratio_test, OMICS_04390 | https://bio.tools/snp_ratio_test | SCR_012070 | 2026-09-12 12:57:44 | 2 | |||||||
|
VirVarSeq Resource Report Resource Website 10+ mentions |
VirVarSeq (RRID:SCR_012116) | software resource | Software for a low frequency Virus Variant detection pipeline for Illumina data. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25178459 | OMICS_05534 | SCR_012116 | 2026-09-12 12:57:45 | 13 | |||||||||
|
Toxtree Resource Report Resource Website 100+ mentions |
Toxtree (RRID:SCR_012086) | software resource | A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach. | standalone software, web app |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18853299 | OMICS_05024 | SCR_012086 | 2026-09-12 12:57:45 | 109 | |||||||||
|
Viewmol Resource Report Resource Website |
Viewmol (RRID:SCR_012088) | software resource | Software providing a graphical front end for computational chemistry programs. | standalone software, windows, c, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
GNU General Public License | OMICS_05057 | https://sources.debian.org/src/viewmol/ | SCR_012088 | 2026-09-12 12:57:45 | 0 | ||||||||
|
Toxmatch Resource Report Resource Website 1+ mentions |
Toxmatch (RRID:SCR_012087) | software resource | A software tool to facilitate chemical similarity calculations. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18617309 | OMICS_05025 | SCR_012087 | 2026-09-12 12:57:45 | 2 |
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