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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
hiCtools Resource Report Resource Website |
hiCtools (RRID:SCR_013010) | hiCtools | software resource | This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00522 | SCR_013010 | 2026-08-01 12:04:54 | 0 | |||||||||
|
LOCAS Resource Report Resource Website 1+ mentions |
LOCAS (RRID:SCR_013064) | LOCAS | software resource | A software to assemble short reads of next generation sequencing technologies at low coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21858125 | OMICS_00019, biotools:locas | https://bio.tools/locas | SCR_013064 | 2026-08-01 12:04:55 | 2 | |||||||
|
VDJFasta Resource Report Resource Website 1+ mentions |
VDJFasta (RRID:SCR_013069) | VDJFasta | software resource | Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19875695 | OMICS_00004 | SCR_013069 | 2026-08-01 12:04:44 | 8 | |||||||||
|
VCAKE Resource Report Resource Website 1+ mentions |
VCAKE (RRID:SCR_013060) | VCAKE | software resource | A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00037 | SCR_013060 | 2026-08-01 12:04:55 | 4 | ||||||||||
|
CoNIFER Resource Report Resource Website 100+ mentions |
CoNIFER (RRID:SCR_013213) | CoNIFER | software resource | Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. |
is listed by: OMICtools has parent organization: SourceForge |
Commercial license | OMICS_00330 | SCR_013213 | Copy Number Inference From Exome Reads | 2026-08-01 12:04:46 | 195 | ||||||||
|
RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | 2026-08-01 12:04:47 | 7 | ||||||||
|
PIA Resource Report Resource Website |
PIA (RRID:SCR_013267) | PIA | software resource | A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00676 | SCR_013267 | 2026-08-01 12:04:46 | 0 | |||||||||
|
miRSeqNovel Resource Report Resource Website 1+ mentions |
miRSeqNovel (RRID:SCR_013257) | miRSeqNovel | software resource | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
Free, Public, Non-commercial | OMICS_00381 | SCR_013257 | 2026-08-01 12:04:46 | 2 | |||||||||
|
AutoMap Resource Report Resource Website 50+ mentions |
AutoMap (RRID:SCR_013095) | AutoMap | software resource | A tool for structural biology and drug design. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01596 | SCR_013095 | 2026-08-01 12:04:45 | 92 | ||||||||||
|
DynamicProg Resource Report Resource Website |
DynamicProg (RRID:SCR_013217) | DynamicProg | software resource | A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01150 | SCR_013217 | 2026-08-01 12:04:57 | 0 | ||||||||||
|
BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-08-01 12:04:47 | 37 | ||||||
|
CongrPE Resource Report Resource Website 1+ mentions |
CongrPE (RRID:SCR_013190) | CongrPE | software resource | A de novo assembly algorithm for Next-Generation Sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00011 | SCR_013190 | 2026-08-01 12:04:56 | 1 | ||||||||||
|
CallSim Resource Report Resource Website |
CallSim (RRID:SCR_013192) | CallSim | software resource | A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Apache License | OMICS_01098 | SCR_013192 | CallSim - Low-volume read processing base corrector | 2026-08-01 12:04:46 | 0 | |||||||
|
SAPAS Resource Report Resource Website 50+ mentions |
SAPAS (RRID:SCR_013195) | SAPAS | software resource | A RNA-seq method for polyA research. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01413 | SCR_013195 | 2026-08-01 12:04:56 | 66 | ||||||||||
|
ArrayOligoSelector Resource Report Resource Website 10+ mentions |
ArrayOligoSelector (RRID:SCR_013494) | ArrayOligoSelector | software resource | Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
PMID:12620119 | Free, Public, Commercial requires license, Use of the blat or gfclient options requires license | OMICS_00826 | SCR_013494 | 2026-08-01 12:04:48 | 13 | ||||||||
|
Ray Meta Resource Report Resource Website 10+ mentions |
Ray Meta (RRID:SCR_011918) | Ray Meta | software resource | Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23259615 | Free | OMICS_01431 | SCR_011918 | 2026-08-01 12:04:33 | 12 | |||||||
|
miRPlant Resource Report Resource Website 10+ mentions |
miRPlant (RRID:SCR_012105) | software resource | A user-friendly plant miRNA prediction tool. | applet, unix/linux, mac os x, windows, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25117656 | GNU General Public License | OMICS_05325, biotools:mirplant | https://bio.tools/mirplant | SCR_012105 | 2026-08-01 12:04:33 | 14 | |||||||
|
PyPedal Resource Report Resource Website 1+ mentions |
PyPedal (RRID:SCR_012104) | software resource | A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_05311 | SCR_012104 | 2026-08-01 12:04:34 | 2 | ||||||||||
|
Simulate PCR Resource Report Resource Website |
Simulate PCR (RRID:SCR_012106) | software resource | Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25005023 | Free, Public | OMICS_05372 | SCR_012106 | 2026-08-01 12:04:33 | 0 | ||||||||
|
SAT-Assembler Resource Report Resource Website 1+ mentions |
SAT-Assembler (RRID:SCR_012108) | software resource | A targeted gene assembly software program which aims to recover gene families of particular interest to biologists. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25122209 | Creative Commons License | OMICS_05397 | SCR_012108 | 2026-08-01 12:04:34 | 3 |
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