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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
FishingCNV Resource Report Resource Website 10+ mentions |
FishingCNV (RRID:SCR_013038) | FishingCNV | software resource | A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23539306 | Commercial license | OMICS_00334 | SCR_013038 | FishingCNV - Copy number variation detection in exome sequencing data, FishingCNV - CNV detection in exome sequencing data, FishingCNV - Copy number variation (CNV) detection in exome sequencing data | 2026-08-01 12:04:55 | 11 | |||||||
|
MSAProbs Resource Report Resource Website 10+ mentions |
MSAProbs (RRID:SCR_012982) | MSAProbs | software resource | An open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20576627 | GNU General Public License, v3 | OMICS_00980 | SCR_012982 | MSAProbs: Multiple Sequence Alignment | 2026-08-01 12:04:54 | 19 | ||||||
|
QcReads Resource Report Resource Website 1+ mentions |
QcReads (RRID:SCR_013002) | QcReads | software resource | Provides an efficient tool for trimming adapter sequences and low quality sequences, in raw reads generated by the high throughput sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01088 | SCR_013002 | 2026-08-01 12:04:54 | 1 | ||||||||||
|
HECTOR Resource Report Resource Website 50+ mentions |
HECTOR (RRID:SCR_013007) | HECTOR | software resource | A parallel multistage k-hopo spectrum based homopolymer-length error corrector for 454 sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01104 | SCR_013007 | HECTOR: Parallel error corrector for 454 datasets | 2026-08-01 12:04:44 | 55 | |||||||||
|
miRDeep* Resource Report Resource Website 10+ mentions |
miRDeep* (RRID:SCR_012960) | miRDeep* | software resource | An integrated application software tool for miRNA identification from RNA sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23221645 | GNU General Public License, v3, Acknowledgement requested | OMICS_00374 | SCR_012960 | 2026-08-01 12:04:42 | 23 | ||||||||
|
AMOS Resource Report Resource Website 1000+ mentions |
AMOS (RRID:SCR_013067) | AMOS | software resource | A collection of tools and class interfaces for the assembly of DNA reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.1093/bib/bbr074 | OMICS_00008, biotools:amos | https://bio.tools/amos, https://sources.debian.org/src/ampliconnoise/ | SCR_013067 | 2026-08-01 12:04:55 | 4769 | |||||||
|
Contrail Resource Report Resource Website 1+ mentions |
Contrail (RRID:SCR_013066) | Contrail | software resource | A Hadoop based genome assembler for assembling large genomes in the clouds. | mapreduce/hadoop |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00012 | SCR_013066 | 2026-08-01 12:04:44 | 5 | |||||||||
|
Easyfig Resource Report Resource Website 1000+ mentions |
Easyfig (RRID:SCR_013169) | Easyfig | software resource | A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI). |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00907 | SCR_013169 | 2026-08-01 12:04:56 | 1101 | ||||||||||
|
ChimeraSlayer Resource Report Resource Website 100+ mentions |
ChimeraSlayer (RRID:SCR_013283) | ChimeraSlayer | software resource | A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01113, biotools:chimeraslayer | https://bio.tools/chimeraslayer | SCR_013283 | 2026-08-01 12:04:46 | 319 | ||||||||
|
Telescoper Resource Report Resource Website |
Telescoper (RRID:SCR_013206) | Telescoper | software resource | An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22962446 | biotools:telescoper, OMICS_00036 | https://bio.tools/telescoper | SCR_013206 | Telescoper - De novo assembly algorithm | 2026-08-01 12:04:45 | 0 | ||||||
|
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 | 2026-08-01 12:04:56 | 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 | 2026-08-01 12:04:56 | 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 | 2026-08-01 12:04:56 | 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 | 2026-08-01 12:04:46 | 0 | ||||||||
|
Celera Genome Browser Resource Report Resource Website |
Celera Genome Browser (RRID:SCR_013093) | Celera Genome Browser | software resource | Software developed at Celera Genomics as part of Celera''s sequencing and annotation of the human genome, and released as open source in 2006. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00904 | SCR_013093 | 2026-08-01 12:04:55 | 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 | 2026-08-01 12:04:46 | 88 | ||||||||||
|
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 | 2026-08-01 12:04:45 | 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 | 2026-08-01 12:04:56 | 100 | |||||||||
|
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 | 2026-08-01 12:04:57 | 0 | |||||||
|
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 | 2026-08-01 12:04:48 | 5 |
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