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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-02-14 02:02:48 | 4 | |||||||||
|
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 | 2026-02-14 02:02:25 | 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 | 2026-02-14 02:02:45 | 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 | 2026-02-14 02:02:25 | 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 | 2026-02-14 02:02:45 | 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 | 2026-02-14 02:02:26 | 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 | 2026-02-14 02:02:26 | 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 | 2026-02-14 02:02:45 | 19 | ||||||
|
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 | 2026-02-14 02:02:20 | 1 | ||||||||||
|
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 | 2026-02-14 02:02:26 | 55 | |||||||||
|
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 | 2026-02-14 02:02:25 | 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 | 2026-02-14 02:02:27 | 4769 | |||||||
|
Contrail Resource Report Resource Website 1+ mentions |
Contrail (RRID:SCR_013066) | Contrail | software resource | A Hadoop based genome assembler for assembling large genomes in the clouds. | mapreduce/hadoop |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00012 | SCR_013066 | 2026-02-14 02:02:46 | 5 | |||||||||
|
Easyfig Resource Report Resource Website 1000+ mentions |
Easyfig (RRID:SCR_013169) | Easyfig | software resource | A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI). |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00907 | SCR_013169 | 2026-02-14 02:02:27 | 1101 | ||||||||||
|
ChimeraSlayer Resource Report Resource Website 100+ mentions |
ChimeraSlayer (RRID:SCR_013283) | ChimeraSlayer | software resource | A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01113, biotools:chimeraslayer | https://bio.tools/chimeraslayer | SCR_013283 | 2026-02-14 02:02:47 | 319 | ||||||||
|
Telescoper Resource Report Resource Website |
Telescoper (RRID:SCR_013206) | Telescoper | software resource | An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22962446 | biotools:telescoper, OMICS_00036 | https://bio.tools/telescoper | SCR_013206 | Telescoper - De novo assembly algorithm | 2026-02-14 02:02:28 | 0 | ||||||
|
palfinder Resource Report Resource Website 1+ mentions |
palfinder (RRID:SCR_013174) | palfinder | software resource | A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads. | pacific biosciences |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00111 | SCR_013174 | 2026-02-14 02:02:46 | 6 | |||||||||
|
sam comp Resource Report Resource Website |
sam comp (RRID:SCR_013179) | sam_comp | software resource | A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | OMICS_00968 | SCR_013179 | 2026-02-14 02:02:46 | 0 | ||||||||
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | heurAA - NGS multiplexed amplicon aligner | 2026-02-14 02:02:28 | 0 | ||||||
|
bisReadMapper Resource Report Resource Website |
bisReadMapper (RRID:SCR_013171) | bisReadMapper | software resource | Fast and lightweight package for mapping bisulfite converted DNA sequencing reads from the Illumina platform. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00576 | SCR_013171 | bisReadMapper - Software for dealing with DNA methylation sequencing data | 2026-02-14 02:02:50 | 0 |
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