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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
DynamicProg Resource Report Resource Website 1+ mentions |
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 | 2026-09-12 12:58:00 | 1 | ||||||||||
|
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 | 2026-09-12 12:58:00 | 38 | ||||||
|
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 | 2026-09-12 12:58:00 | 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 | 2026-09-12 12:58:00 | 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 | 2026-09-12 12:58:00 | 68 | ||||||||||
|
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 | 2026-09-12 12:58:03 | 13 | ||||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-09-12 12:57:41 | 312 | |||||
|
TagCleaner Resource Report Resource Website 50+ mentions |
TagCleaner (RRID:SCR_011846) | software application, software resource, standalone software, web application | A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets. | tag sequence, standalone software, web application, microbiome, genomic, metagenomic, datasets |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: SourceForge |
Available for download | OMICS_01094 | SCR_011846 | 2026-09-12 12:57:41 | 65 | |||||||||
|
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 | 2026-09-12 12:57:42 | 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 | 2026-09-12 12:57:45 | 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 | 2026-09-12 12:57:45 | 3 | ||||||||||
|
Simulate PCR Resource Report Resource Website 1+ mentions |
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 | 2026-09-12 12:57:45 | 2 | ||||||||
|
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 | 2026-09-12 12:57:45 | 3 | ||||||||
|
FingerID Resource Report Resource Website 10+ mentions |
FingerID (RRID:SCR_012077) | software resource | A metabolite identification software using tandem mass spectrometry and kernel methods. | standalone software, matlab, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815355 | GNU General Public License | OMICS_04649 | SCR_012077 | 2026-09-12 12:57:45 | 23 | ||||||||
|
proTRAC Resource Report Resource Website 10+ mentions |
proTRAC (RRID:SCR_012078) | software resource | A software which detects and analyses piRNA clusters based on quantifiable deviations from a hypothetical uniform distribution regarding the decisive piRNA cluster characteristics. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22233380 | Creative Commons License | OMICS_04874 | SCR_012078 | probabilistic TRacking and Analysis of Clusters | 2026-09-12 12:57:45 | 28 | |||||||
|
diCal-IBD Resource Report Resource Website |
diCal-IBD (RRID:SCR_012111) | software resource | Software tool for detecting identity-by-descent (IBD) tracts between pairs of genomic sequences. | standalone software, unix/linux, mac os x, windows, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25147361 | BSD License | OMICS_05459 | SCR_012111 | 2026-09-12 12:57:45 | 0 | ||||||||
|
Ionwinze Resource Report Resource Website |
Ionwinze (RRID:SCR_012115) | software resource | Software tool to pick out ion signals that discriminate two groups of samples (e.g. diseased/healthy, resistant/susceptible) by quasi-datapoint-wise comparison using univariate statistic procedures. | standalone software, windows, c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24004415 | GNU General Public License | OMICS_05522 | SCR_012115 | 2026-09-12 12:57:45 | 0 | ||||||||
|
NetMODE Resource Report Resource Website 1+ mentions |
NetMODE (RRID:SCR_012085) | software resource | Fast motif detection algorithm for subgraph size no more than 6. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23272055 | OMICS_05019 | SCR_012085 | 2026-09-12 12:57:45 | 1 | |||||||||
|
SketchEl Resource Report Resource Website |
SketchEl (RRID:SCR_012082) | software resource | An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. | applet, mac os x, unix/linux, windows, java, javascript |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License | OMICS_04982 | SCR_012082 | 2026-09-12 12:57:45 | 0 | |||||||||
|
HopeMap Resource Report Resource Website |
HopeMap (RRID:SCR_012081) | software resource | A connected-components based fast algorithm for network alignment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23710435 | OMICS_04896 | SCR_012081 | 2026-09-12 12:57:45 | 0 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
