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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Genovar Resource Report Resource Website 1+ mentions |
Genovar (RRID:SCR_010930) | Genovar | software resource | A Detection and Visualization software tool for Genomic Variants. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Korea National Institute of Health |
Free, Public | OMICS_00724, biottools:genovar | https://bio.tools/genovar | SCR_010930 | 2026-08-01 12:04:18 | 1 | |||||||
|
MAnorm Resource Report Resource Website 100+ mentions |
MAnorm (RRID:SCR_010869) | MAnorm | software resource | A robust software package for quantitative comparison of ChIP-Seq data sets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute |
PMID:22424423 | OMICS_00467, biotools:manorm | https://bio.tools/manorm | SCR_010869 | Manorm - a robust model for quantitative comparison of ChIP-Seq data sets | 2026-08-01 12:03:59 | 111 | ||||||
|
MeRIP-PF Resource Report Resource Website 1+ mentions |
MeRIP-PF (RRID:SCR_010904) | MeRIP-PF | software resource | A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:merip-pf, OMICS_00571 | https://bio.tools/merip-pf | SCR_010904 | MeRIP-Seq Peak-Finding Program | 2026-08-01 12:04:00 | 3 | |||||||
|
BatMeth Resource Report Resource Website 1+ mentions |
BatMeth (RRID:SCR_010906) | BatMeth | software resource | Improved mapper for bisulfite sequencing reads on DNA methylation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
biotools:batmeth, OMICS_00574 | https://bio.tools/batmeth | SCR_010906 | 2026-08-01 12:04:18 | 1 | ||||||||
|
QUMA Resource Report Resource Website 100+ mentions |
QUMA (RRID:SCR_010907) | QUMA | software resource | You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00588, biotools:quma | https://bio.tools/quma | SCR_010907 | QUantification tool for Methylation Analysis | 2026-08-01 12:04:00 | 364 | |||||||
|
PeakRanger Resource Report Resource Website 10+ mentions |
PeakRanger (RRID:SCR_010863) | PeakRanger | software resource | Software for a multi-purpose ChIP Seq peak caller. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21554709 | OMICS_00451, biotools:peakranger | https://bio.tools/peakranger | SCR_010863 | 2026-08-01 12:03:59 | 21 | |||||||
|
SEAL Resource Report Resource Website 100+ mentions |
SEAL (RRID:SCR_010914) | SEAL | software resource | A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21697132 | biotools:seal, OMICS_00682 | https://bio.tools/seal | SCR_010914 | 2026-08-01 12:04:01 | 121 | |||||||
|
DIME Resource Report Resource Website 10+ mentions |
DIME (RRID:SCR_010874) | DIME | software resource | R-package for identifying differential ChIP-seq based on an ensemble of mixture models. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:DIME, OMICS_00473 | https://bio.tools/DIME | SCR_010874 | 2026-08-01 12:04:18 | 29 | ||||||||
|
CloudBurst Resource Report Resource Website |
CloudBurst (RRID:SCR_010911) | CloudBurst | software resource | A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19357099 | Free | OMICS_00657, biotools:cloudburst | https://bio.tools/cloudburst | SCR_010911 | 2026-08-01 12:04:00 | 0 | ||||||
|
SLIQ Resource Report Resource Website 1+ mentions |
SLIQ (RRID:SCR_005003) | SLIQ | software resource | Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph. | python, scaffolding, contig position, contig orientation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Rutgers University; New Jersey; USA |
PMID:23057825 | biotools:sliq, OMICS_00048 | https://bio.tools/sliq | SCR_005003 | Simple linear inequalities, SLiQ: Simple linear inequalities based Mate-Pair reads filtering and scaffolding | 2026-08-01 12:02:51 | 3 | ||||||
|
SOPRA Resource Report Resource Website 10+ mentions |
SOPRA (RRID:SCR_005035) | SOPRA | software resource | Software tool to exploit the mate pair/paired-end information for assembly of short reads from high throughput sequencing platforms, e.g. Illumina and SOLiD. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Rutgers University; New Jersey; USA |
PMID:20576136 | Acknowledgement requested | biotools:sopra, OMICS_00049 | https://bio.tools/sopra | SCR_005035 | SOPRA - Statistical Optimization of Paired Read Assembly, Statistical Optimization of Paired Read Assembly | 2026-08-01 12:02:48 | 20 | |||||
|
SSPACE Resource Report Resource Website 100+ mentions |
SSPACE (RRID:SCR_005056) | SSPACE | software resource | A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. | scaffolding, contig, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21149342 DOI:10.1093/bioinformatics/btq683 |
GNU General Public License, Registration required | biotools:sspace, OMICS_00050 | https://bio.tools/sspace, https://sources.debian.org/src/sspace/ | SCR_005056 | 2026-08-01 12:02:53 | 426 | ||||||
|
MBCluster.Seq Resource Report Resource Website 1+ mentions |
MBCluster.Seq (RRID:SCR_005079) | MBCluster.Seq | software resource | Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24191069 | GNU General Public License, >/=v3 | OMICS_01417, biotools:mbcluster.seq | https://bio.tools/mbcluster.seq | SCR_005079 | MBCluster.Seq: Model-Based Clustering for RNA-seq Data | 2026-08-01 12:02:48 | 1 | |||||
|
GRASS Resource Report Resource Website 50+ mentions |
GRASS (RRID:SCR_005071) | GRASS | software resource | A generic algorithm for scaffolding next-generation sequencing assemblies. | next-generation sequencing, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22492642 | GNU General Public License, v3 | biotools:GRASS, OMICS_00043 | https://bio.tools/GRASS | SCR_005071 | GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies, GeneRic ASembly Scaffolder | 2026-08-01 12:02:48 | 89 | |||||
|
G-BLASTN Resource Report Resource Website |
G-BLASTN (RRID:SCR_005062) | G-BLASTN | software resource | A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. | parallel computation 4, blast, alignment, nucleotide, gpu, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BLAST has parent organization: Hong Kong Baptist University; Hong Kong; China has parent organization: SourceForge |
Hong Kong Baptist University; Hong Kong; China FRG2/11-12/158; NVIDIA |
PMID:24463183 | Free | OMICS_02263, biotools:g-blastn | http://sourceforge.net/projects/gblastn/, https://bio.tools/g-blastn | SCR_005062 | 2026-08-01 12:02:45 | 0 | |||||
|
VFS Resource Report Resource Website 1+ mentions |
VFS (RRID:SCR_005138) | VFS | software resource | A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. | ubuntu, debian, high-throughput sequencing, virus, reconstruct, fusion transcript, transcript, integration, fusion, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23314323 | GNU General Public License, v3 | OMICS_00224, biotools:viralfusionseq | https://bio.tools/viralfusionseq | SCR_005138 | ViralFusionSeq, ViralFusionSeq (VFS) | 2026-08-01 12:02:56 | 1 | |||||
|
MMAPPR Resource Report Resource Website 1+ mentions |
MMAPPR (RRID:SCR_005092) | MMAPPR | software resource | A software analysis pipeline for mapping mutations using RNA-seq that works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome. In addition, it compensates for the considerable amount of noise in RNA-seq datasets and simultaneously identifies the region where the mutation lies and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can utilize RNA-seq datasets from isolated tissues or whole organisms that are often generated for phenotypic analysis and gene network analysis in novel mutants. | mutation, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
PMID:23299975 | Acknowledgement requested | OMICS_01361, biotools:mmappr | https://bio.tools/mmappr | SCR_005092 | Mutation Mapping Analysis Pipeline for Pooled RNA-seq | 2026-08-01 12:02:45 | 7 | |||||
|
FusionMap Resource Report Resource Website 50+ mentions |
FusionMap (RRID:SCR_005242) | FusionMap | software resource | An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI. | windows, linux, c#, fusion gene, next-generation sequencing, gene, reference indexing, read filtering, fusion alignment, reporting, alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21593131 | Free, Non-commercial | biotools:fusionmap, OMICS_00316 | https://bio.tools/fusionmap | SCR_005242 | 2026-08-01 12:02:51 | 88 | ||||||
|
rQuant Resource Report Resource Website 1+ mentions |
rQuant (RRID:SCR_005150) | rQuant | software resource | Software for quantitative detection of alternative transcripts with RNA-Seq data. The method, based on quadratic programming, estimates biases introduced by experimental settings and is thus a powerful tool to reveal and quantify novel (alternative) transcripts. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy |
PMID:20551130 | biotools:rquant.web, OMICS_01286 | https://bio.tools/rquant.web | SCR_005150 | rQuant: quantitative detection of alternative transcripts with RNA-Seq data | 2026-08-01 12:02:49 | 1 | ||||||
|
ShoRAH Resource Report Resource Website 10+ mentions |
ShoRAH (RRID:SCR_005211) | ShoRAH | software resource | A software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. | linux, mac os x, windows, next-generation sequencing, c++, python, perl, structure, population, short sequence read, haplotype, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21521499 | GNU General Public License, v3 | biotools:shorah, OMICS_00231 | https://bio.tools/shorah | SCR_005211 | Short Reads Assembly into Haplotypes, ShoRAH - Short Reads Assembly into Haplotypes | 2026-08-01 12:02:48 | 35 |
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