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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
dna-bison Resource Report Resource Website 1+ mentions |
dna-bison (RRID:SCR_005913) | dna-bison | software resource | Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00582 | SCR_005913 | 2026-09-03 04:48:41 | 1 | ||||||||||
|
Trowel Resource Report Resource Website 1+ mentions |
Trowel (RRID:SCR_012890) | Trowel | software resource | An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. | c++, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Apache License | OMICS_01111, biotools:trowel | https://bio.tools/trowel/ | SCR_012890 | Trowel - Error Correction Module for Illumina Sequencing Reads, Trowel - Sequencing Error Corrector | 2026-09-03 04:51:43 | 5 | ||||||
|
Onco-STS Resource Report Resource Website |
Onco-STS (RRID:SCR_012990) | Onco-STS | software resource | Software for a web-based Laboratory Information Management System for sample and analysis tracking in oncogenomic experiments. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01008 | SCR_012990 | Onco-STS - A web-based Laboratory Information Management System | 2026-09-03 04:51:46 | 0 | ||||||||
|
NxGview Resource Report Resource Website |
NxGview (RRID:SCR_012994) | NxGview | software resource | A virtual software pipeline that contains several PERL modules for processing next generation sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01065 | SCR_012994 | 2026-09-03 04:52:03 | 0 | ||||||||||
|
Bamformatics Resource Report Resource Website 1+ mentions |
Bamformatics (RRID:SCR_013041) | Bamformatics | software resource | Software that provides a coherent and consistent approach to analysis of high-throughput sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00283 | SCR_013041 | Bamformatics - Toolkit and GUI for sequencing data analysis | 2026-09-03 04:51:54 | 1 | ||||||||
|
BSmapper Resource Report Resource Website |
BSmapper (RRID:SCR_012998) | BSmapper | software resource | Sequence mapper for bisulfite sequencing reads for DNA methylation studies. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00580 | SCR_012998 | 2026-09-03 04:52:25 | 0 | |||||||||
|
MendelScan Resource Report Resource Website 1+ mentions |
MendelScan (RRID:SCR_013053) | MendelScan | software resource | A software tool for prioritizing candidate variants in family-based studies of inherited disease. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00065 | SCR_013053 | MendelScan - Variant scoring and linkage mapping for family exome sequencing | 2026-09-03 04:52:27 | 4 | |||||||
|
ProbeSelect Resource Report Resource Website 1+ mentions |
ProbeSelect (RRID:SCR_012965) | ProbeSelect | software resource | Software for selecting probes in heterogenous transcriptional sets. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00836 | SCR_012965 | ProbeSelect - Selecting probes in heterogenous transcriptional sets | 2026-09-03 04:52:24 | 5 | |||||||||
|
SeqGenome Browser Resource Report Resource Website |
SeqGenome Browser (RRID:SCR_012970) | SeqGenome Browser | software resource | Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00924 | SCR_012970 | 2026-09-03 04:52:01 | 0 | ||||||||
|
miRDeep-P Resource Report Resource Website 1+ mentions |
miRDeep-P (RRID:SCR_013026) | miRDP | software resource | A computational tool for analyzing the microRNA (miRNA) transcriptome in plants. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21775303 | GNU General Public License, v3 | OMICS_00375 | SCR_013026 | 2026-09-03 04:52:03 | 6 | ||||||||
|
KungFq Resource Report Resource Website |
KungFq (RRID:SCR_012979) | KungFq | software resource | Tool that compresses and decompresses fastq files. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23221092 | OMICS_00962 | SCR_012979 | 2026-09-03 04:52:06 | 0 | |||||||||
|
ncPRO-seq Resource Report Resource Website 1+ mentions |
ncPRO-seq (RRID:SCR_013031) | ncPRO-seq | software resource | Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23044543 | OMICS_00366 | SCR_013031 | ncPRO-seq - A tool for annotation and profiling of ncRNAs from small RNA sequencing data | 2026-09-03 04:52:26 | 9 | ||||||||
|
vcf2MSAT Resource Report Resource Website |
vcf2MSAT (RRID:SCR_013034) | vcf2MSAT | software resource | A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00118 | SCR_013034 | vcf2MSAT - Find Microsatellites in a .vcf report | 2026-09-03 04:52:09 | 0 | |||||||||
|
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 | 2026-09-03 04:51:49 | 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 | 2026-09-03 04:51:46 | 20 | ||||||
|
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 | 2026-09-03 04:51:47 | 1 | ||||||||||
|
RDP FrameBot Resource Report Resource Website 1+ mentions |
RDP FrameBot (RRID:SCR_013083) | FrameBot | analysis service resource, data analysis service, production service resource, service resource, software resource | A frameshift correction and nearest neighbor classification tool for use with high-throughput amplicon sequencing. It uses a dynamic programming algorithm to align each query DNA sequence against a set of target protein sequences, produces frameshift-corrected protein and DNA sequences and an optimal global or local protein alignment. It also helps filter out non-target reads. The online version of FrameBot is available on http://fungene.cme.msu.edu/FunGenePipeline. |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Michigan State University; Michigan; USA |
PMID:24045641 | OMICS_01527 | SCR_013083 | RDP_FrameBot | 2026-09-03 04:52:11 | 2 | ||||||||
|
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 | 2026-09-03 04:52:25 | 56 | |||||||||
|
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 | 2026-09-03 04:51:59 | 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 | 2026-09-03 04:52:06 | 4855 |
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