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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
miRExpress Resource Report Resource Website 10+ mentions |
miRExpress (RRID:SCR_010831) | miRExpress | software resource | A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
OMICS_00379 | SCR_010831 | 2026-02-07 02:08:02 | 49 | ||||||||||
|
HugeSeq Resource Report Resource Website 10+ mentions |
HugeSeq (RRID:SCR_010803) | HugeSeq | software resource | An automated pipeline for detecting genetic variants from High-throUghput GEnome SEQuencing. | is listed by: OMICtools | OMICS_00288 | SCR_010803 | 2026-02-07 02:08:05 | 10 | ||||||||||
|
MutFinder Resource Report Resource Website |
MutFinder (RRID:SCR_010804) | MutFinder | software resource | It streamlines the next generation sequencing data analysis using BFAST for aligner, SAMTOOLS for SNP caller, and ANNOVAR for annotation. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_00290 | SCR_010804 | Mutation finder in DNA-seq | 2026-02-07 02:08:01 | 0 | |||||||||
|
SIMPLEX Resource Report Resource Website 10+ mentions |
SIMPLEX (RRID:SCR_010807) | SIMPLEX | software resource | Cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. | is listed by: OMICtools | OMICS_00294 | SCR_010807 | 2026-02-07 02:08:05 | 21 | ||||||||||
|
WEP Resource Report Resource Website |
WEP (RRID:SCR_010809) | WEP | software resource | A complete whole-exome sequencing pipeline and provides easy access through interface to intermediate and final results. | is listed by: OMICtools | OMICS_00296 | SCR_010809 | 2026-02-07 02:07:52 | 0 | ||||||||||
|
MoDIL Resource Report Resource Website 1+ mentions |
MoDIL (RRID:SCR_010764) | MoDIL | software resource | Software for a novel method for finding medium sized indels from high throughput sequencing datasets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
OMICS_00066, biotools:modil | https://bio.tools/modil | SCR_010764 | MoDIL: Detecting INDEL Variation with Clone-end Sequencing | 2026-02-07 02:08:04 | 4 | |||||||
|
MISA Resource Report Resource Website 500+ mentions |
MISA (RRID:SCR_010765) | MISA | software resource | Software tool that allows the identification and localization of perfect microsatellites as well as compound microsatellites which are interrupted by a certain number of bases. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00110, biotools:misa | https://bio.tools/misa | SCR_010765 | MISA - MIcroSAtellite identification tool | 2026-02-07 02:07:52 | 920 | |||||||
|
T-REKS Resource Report Resource Website 10+ mentions |
T-REKS (RRID:SCR_010768) | T-REKS | software resource | An algorithm for de novo detection and alignment of repeats in sequences based on K-means algorithm. | matlab | is listed by: OMICtools | PMID:19671691 | OMICS_00116 | SCR_010768 | 2026-02-07 02:07:52 | 17 | ||||||||
|
GensearchNGS Resource Report Resource Website 10+ mentions |
GensearchNGS (RRID:SCR_010802) | GensearchNGS | software resource | An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Commercial license | OMICS_00287, biotools:gensearchngs | https://bio.tools/gensearchngs | SCR_010802 | 2026-02-07 02:07:52 | 21 | |||||||
|
AgileVariantMapper Resource Report Resource Website 1+ mentions |
AgileVariantMapper (RRID:SCR_010770) | AgileVariantMapper | software resource | Software that visualises sequence variant data from whole exome data, so that it is possible to identify autozygous regions in consanguineous individuals. | is listed by: OMICtools | PMID:23090942 | OMICS_00122 | SCR_010770 | AgileVariantMapper - Autozygosity mapping using Next generation sequence data | 2026-02-07 02:08:01 | 1 | ||||||||
|
HomSI Resource Report Resource Website 1+ mentions |
HomSI (RRID:SCR_010771) | HomSI | software resource | A software tool that identifies homozygous regions using deep sequence data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24307702 | Free | OMICS_00124, biotools:homsi | https://bio.tools/homsi | SCR_010771 | Homozygous Stretch Identifier from next-generation sequencing data, HomSI - Homozygous Stretch Identifier from next-generation sequencing data | 2026-02-07 02:07:52 | 3 | |||||
|
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 | 2026-02-07 02:08:02 | 280 | ||||||||
|
ExomeCNV Resource Report Resource Website 50+ mentions |
ExomeCNV (RRID:SCR_010815) | ExomeCNV | software resource | A statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies from mapped short sequence reads in exome sequencing data. | is listed by: OMICtools | OMICS_00333 | SCR_010815 | 2026-02-07 02:07:53 | 59 | ||||||||||
|
CNAnorm Resource Report Resource Website 10+ mentions |
CNAnorm (RRID:SCR_010816) | CNAnorm | software resource | A Bioconductor package to estimate Copy Number Aberrations (CNA) in cancer samples. | is listed by: OMICtools | OMICS_00336 | SCR_010816 | 2026-02-07 02:08:05 | 15 | ||||||||||
|
CNValidator Resource Report Resource Website |
CNValidator (RRID:SCR_010819) | CNValidator | software resource | Identifies high quality CNVs based on the density of homozygous SNPs and the ratio of heterozygous SNP reads. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_00340 | SCR_010819 | cnvalidator - a package for identification of high quality copy-number variations | 2026-02-07 02:08:05 | 0 | |||||||||
|
breseq Resource Report Resource Website 100+ mentions |
breseq (RRID:SCR_010810) | breseq | software resource | A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes. | windows, genomics, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
OMICS_00298, biotools:breseq | https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing https://bio.tools/breseq |
SCR_010810 | breseq - Determine mutations in evolved microbes from next-generation sequencing data | 2026-02-07 02:08:05 | 391 | |||||||
|
MutSig Resource Report Resource Website 100+ mentions |
MutSig (RRID:SCR_010779) | MutSig | software resource | Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:23770567 | OMICS_00155, biotools:MutSig2CV | https://bio.tools/MutSig2CV | SCR_010779 | Mutation Significance | 2026-02-07 02:08:01 | 127 | ||||||
|
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 | 2026-02-07 02:07:53 | 22 | |||||
|
PhD-SNP Resource Report Resource Website 100+ mentions |
PhD-SNP (RRID:SCR_010782) | PhD-SNP | software resource | It is based a SVM-based classifier. | is listed by: OMICtools | PMID:16895930 | OMICS_00158 | SCR_010782 | Predictor of human Deleterious Single Nucleotide Polymorphisms | 2026-02-07 02:08:01 | 286 | ||||||||
|
PMut Resource Report Resource Website 50+ mentions |
PMut (RRID:SCR_010783) | PMut | software resource | A software aimed at the annotation and prediction of pathological mutations. | is listed by: OMICtools | PMID:15390262 | OMICS_00159 | SCR_010783 | 2026-02-07 02:08:04 | 80 |
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