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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-02-14 02:02:05 | 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 | 2026-02-14 02:01:50 | 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 | 2026-02-14 02:02:05 | 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 | 2026-02-14 02:02:06 | 424 | |||||||
|
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 | 2026-02-14 02:01:49 | 128 | ||||||
|
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 | 2026-02-14 02:01:50 | 23 | |||||
|
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 | 2026-02-14 02:02:04 | 293 | ||||||||
|
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 | 2026-02-14 02:01:49 | 80 | |||||||||
|
Integra Life Sciences Resource Report Resource Website 100+ mentions |
Integra Life Sciences (RRID:SCR_010741) | commercial organization | Commercial tissue bank for human tissues. | life science, organization, commercial, surgical instrument, neurosurgery | Commercial | grid.481865.6, nlx_97702 | https://ror.org/04t8qhn97 | SCR_010741 | Integra | 2026-02-14 02:01:48 | 384 | ||||||||
|
ALLPATHS-LG Resource Report Resource Website 100+ mentions |
ALLPATHS-LG (RRID:SCR_010742) | ALLPATHS-LG | software resource | Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. | genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:21187386 | OMICS_00007, biotools:allpaths-lg | https://bio.tools/allpaths-lg | SCR_010742 | 2026-02-14 02:02:02 | 237 | |||||||
|
Celera assembler Resource Report Resource Website 50+ mentions |
Celera assembler (RRID:SCR_010750) | Celera assembler | software resource | A de novo whole-genome shotgun (WGS) DNA sequence assembler. |
is listed by: OMICtools is related to: Canu has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00009 | SCR_010750 | 2026-02-14 02:01:49 | 56 | |||||||||
|
SOAPdenovo Resource Report Resource Website 1000+ mentions |
SOAPdenovo (RRID:SCR_010752) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, rna, dna, de novo, genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20019144 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soapdenovo, OMICS_00031, SCR_014986 | https://github.com/aquaskyline/SOAPdenovo2 https://bio.tools/soapdenovo https://sources.debian.org/src/soapdenovo/ |
SCR_010752 | SOAPdenovo2 | 2026-02-14 02:02:04 | 1299 | ||||||
|
SUTTA Resource Report Resource Website |
SUTTA (RRID:SCR_010754) | SUTTA | software resource | A new De Novo DNA sequence assembler based on global search-methods in order to contain the complexity of the assembly problem. | is listed by: OMICtools | OMICS_00034 | SCR_010754 | 2026-02-14 02:01:49 | 0 | ||||||||||
|
Atlas2 Resource Report Resource Website 10+ mentions |
Atlas2 (RRID:SCR_010756) | software resource | A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Baylor University; Texas; USA |
PMID:22239737 | biotools:atlas_suite, OMICS_00051 | https://bio.tools/atlas_suite | SCR_010756 | Atlas Suite | 2026-02-14 02:02:04 | 11 | |||||||
|
FamSeq Resource Report Resource Website |
FamSeq (RRID:SCR_010760) | FamSeq | software resource | A computational tool for calculating probability of variants in family-based sequencing data. | c++ |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
PMID:23426633 | OMICS_00058 | SCR_010760 | Family-Based Sequencing Program | 2026-02-14 02:02:05 | 0 | |||||||
|
GenePix Pro Resource Report Resource Website 500+ mentions |
GenePix Pro (RRID:SCR_010969) | GenePix Pro | software resource | Industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and intuitive workflows. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00840 | SCR_010969 | 2026-02-14 02:01:52 | 627 | ||||||||||
|
OligoArray Resource Report Resource Website 10+ mentions |
OligoArray (RRID:SCR_010961) | OligoArray | software resource | A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:12799432 | OMICS_00828, biotools:oligoarray | https://bio.tools/oligoarray | SCR_010961 | OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach, OligoArray 2.1: Genome-scale oligonucleotide design for microarrays | 2026-02-14 02:01:52 | 38 | ||||||
|
Picky Resource Report Resource Website 10+ mentions |
Picky (RRID:SCR_010963) | Picky | software resource | A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. |
is listed by: OMICtools has parent organization: Iowa State University; Iowa; USA |
NSF DBI0850195 | PMID:15180932 PMID:19849862 PMID:20406469 |
Free, Public, Acknowledgement requested | OMICS_00833 | SCR_010963 | Picky: Optimal Oligonucleotide Design and Analysis | 2026-02-14 02:02:07 | 37 | ||||||
|
ROSO Resource Report Resource Website 1+ mentions |
ROSO (RRID:SCR_010967) | ROSO | software resource | A software to design optimized oligonucleotide probes (size over 25 nucleotides) for microarrays. |
is listed by: OMICtools has parent organization: PRABI |
PMID:14734320 | Free to non-profit users, On request | OMICS_00838 | SCR_010967 | ROSO - A friend for your design, Recherche et Optimisation de Sondes Oligonucl��otidiques, Recherche et Optimisation de Sondes Oligonucleotidiques | 2026-02-14 02:02:07 | 1 | |||||||
|
HMCan Resource Report Resource Website 10+ mentions |
HMCan (RRID:SCR_010858) | HMCan | software resource | A Hidden Markov Model based software tool that is developed to detect histone modification in cancer ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:24021381 | biotools:hmcan, OMICS_00443 | https://bio.tools/hmcan | SCR_010858 | Histone Modification in Cancer | 2026-02-14 02:02:06 | 13 |
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