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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Micro-Analyzer Resource Report Resource Website |
Micro-Analyzer (RRID:SCR_000394) | Micro-Analyzer | software resource | Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems. | windows, linux, java, java swing, gene expression, snp, microarray, affymetrix, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23731720 | Free, Available for download, Freely available | OMICS_01919, biotools:microanalyzer | https://bio.tools/microanalyzer | SCR_000394 | microAnalyzer | 2026-09-19 12:49:22 | 0 | |||||
|
SAMBLASTER Resource Report Resource Website 10+ mentions |
SAMBLASTER (RRID:SCR_000468) | software resource | Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Virginia; Virginia; USA |
PMID:24812344 DOI:10.1093/bioinformatics/btu314 |
Free, Available for download, Freely available | biotools:samblaster, OMICS_04682 | https://bio.tools/samblaster, https://sources.debian.org/src/samblaster/ | SCR_000468 | 2026-09-19 12:49:24 | 19 | |||||||
|
nmrML Resource Report Resource Website 1+ mentions |
nmrML (RRID:SCR_000467) | nmrML | data or information resource, interchange format, markup language, narrative resource, standard specification | An open mark-up language for NMR data. | nuclear magnetic resonance, bio.tools |
is listed by: bio.tools is listed by: Debian is parent organization of: nmrCV |
nlx_157309, biotools:nmrml_converter | https://bio.tools/nmrml_converter | SCR_000467 | 2026-09-19 12:49:24 | 9 | ||||||||
|
TAPyR Resource Report Resource Website 1+ mentions |
TAPyR (RRID:SCR_000588) | software resource | An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies. | gs flx, genome analyzer, bwt, fasta, fastq, sff formats, pyrosequencing reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21672185 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tapyr, OMICS_00693 | https://bio.tools/tapyr | SCR_000588 | Tool for Alignment of Pyrosequencing Reads | 2026-09-19 12:49:26 | 1 | ||||||
|
MuTect Resource Report Resource Website 100+ mentions |
MuTect (RRID:SCR_000559) | MuTect | software resource | Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. | next-generation sequencing, somatic mutation, tumor, normal, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Cancer | PMID:23396013 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mutect, OMICS_00087 | https://bio.tools/mutect | SCR_000559 | Mutect | 2026-09-19 12:49:25 | 102 | ||||
|
SRMA Resource Report Resource Website |
SRMA (RRID:SCR_000669) | SRMA | software resource | A post-alignment micro re-aligner for next-generation high throughput sequencing data. | matlab, sequence re-alignment, command-line, java, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20932289 | Free, Available for download, Freely available | biotools:srma, OMICS_01079 | https://bio.tools/srma | SCR_000669 | Short Read Micro re-Aligner | 2026-09-19 12:49:27 | 0 | |||||
|
ShortFuse Resource Report Resource Website 1+ mentions |
ShortFuse (RRID:SCR_001107) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2. | fusion transcripts, rna, sequence data, python 2, c++, sequence analysis software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21330288 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:shortfuse, OMICS_01355 | https://bio.tools/shortfuse | SCR_001107 | 2026-09-19 12:49:34 | 1 | |||||||
|
CUDA-EC Resource Report Resource Website 1+ mentions |
CUDA-EC (RRID:SCR_001090) | CUDA-EC | software resource | A fast parallel error correction tool for short reads. | c, gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20426693 | Free, Available for download, Freely available | OMICS_01100, biotools:cuda-ec | https://bio.tools/cuda-ec | SCR_001090 | Compute Unified Device Architecture | 2026-09-19 12:49:34 | 1 | |||||
|
DSRC Resource Report Resource Website 1+ mentions |
DSRC (RRID:SCR_001005) | DSRC | data management software, software application, software resource | An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression. | fastq, dna sequence, compression, multithread, data management software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21252073 | Free, Available as binary, Available as source code | biotools:dsrc, OMICS_00955 | https://bio.tools/dsrc | SCR_001005 | DNA Sequence Reads Compression, DNA Sequence Reads Compression (DSRC) | 2026-09-19 12:49:33 | 1 | |||||
|
GimmeMotifs Resource Report Resource Website 1+ mentions |
GimmeMotifs (RRID:SCR_001146) | GimmeMotifs | software resource | Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | linux, chip-seq, motif, cluster, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:21081511 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gimmemotifs, OMICS_02150 | https://bio.tools/gimmemotifs | SCR_001146 | GimmeMotifs: a systematic de novo motif prediction pipeline | 2026-09-19 12:49:35 | 4 | |||||
|
Illuminator Resource Report Resource Website |
Illuminator (RRID:SCR_001019) | data analysis software, data processing software, sequence analysis software, software application, software resource | A sequence alignment program for the output from Illumina GA-II clonal sequencers. It uses an algorithm that indexes the reference sequence as a series of 8-mers and then matches the genomic reads to the 8-mer index, in a mutation-tolerant way permitting identification of single-nucleotide substitutions and indels. | sequence analysis software, sequence alignment, software, mutation detection, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Leeds; West Yorkshire; United Kingdom |
PMID:21621601 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:illuminator, OMICS_02165 | https://bio.tools/illuminator | SCR_001019 | 2026-09-19 12:49:33 | 0 | |||||||
|
Visualization and Analysis of Networks containing Experimental Data (VANTED) Resource Report Resource Website 10+ mentions |
Visualization and Analysis of Networks containing Experimental Data (VANTED) (RRID:SCR_001138) | VANTED | data analysis software, data processing software, data visualization software, software application, software resource | Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data. | binary executable, simulation software, signal processing software, java, network visualization, statistical analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:23140568 | Open source | biotools:vanted, nif-0000-00373 | https://bitbucket.org/vanted-dev/vanted/src, https://bio.tools/vanted | http://vanted.ipk-gatersleben.de/ | SCR_001138 | Visualization and Analysis of Networks containing Experimental Data, VANTED v2 | 2026-09-19 12:49:35 | 14 | ||||
|
rbsurv Resource Report Resource Website 1+ mentions |
rbsurv (RRID:SCR_001175) | rbsurv | software resource | Software package that selects genes associated with survival. | microarray, gene, survival, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:rbsurv, BioTools:rbsurv, OMICS_02088 | https://bio.tools/rbsurv, https://bio.tools/rbsurv, https://bio.tools/rbsurv | SCR_001175 | rbsurv - Robust likelihood-based survival modeling with microarray data | 2026-09-19 12:49:36 | 1 | ||||||
|
wateRmelon Resource Report Resource Website 100+ mentions |
wateRmelon (RRID:SCR_001296) | wateRmelon | software resource | Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages. | dna methylation, microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23631413 | Free, Available for download, Freely available | OMICS_02039, biotools:watermelon | https://bio.tools/watermelon | SCR_001296 | 2026-09-19 12:49:38 | 314 | ||||||
|
Sherman Resource Report Resource Website 100+ mentions |
Sherman (RRID:SCR_001294) | Sherman | software resource | Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments. | perl, bisulfite sequencing, high-throughput sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
Free, Available for download, Freely available | biotools:sherman, OMICS_02041 | http://www.bioinformatics.babraham.ac.uk/projects/sherman/ | SCR_001294 | Sherman - bisulfite-treated Read FastQ Simulator | 2026-09-19 12:49:38 | 124 | ||||||
|
GenomicTools Resource Report Resource Website |
GenomicTools (RRID:SCR_001205) | GenomicTools | software resource | A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor. | high-throughput sequencing, rna-seq, chip-seq, genomics, sequencing, hi-c, epigenetics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:22113082 | Free, Available for download, Freely available | biotools:genomictools, OMICS_02144 | https://bio.tools/genomictools | SCR_001205 | GenomicTools: a computational platform for developing high-throughput analytics in genomics. | 2026-09-19 12:49:36 | 0 | |||||
|
PARalyzer Resource Report Resource Website 1+ mentions |
PARalyzer (RRID:SCR_001208) | PARalyzer | software resource | Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites. | interaction, rna-binding protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Duke University; North Carolina; USA |
PMID:21851591 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:paralyzer, OMICS_02137 | https://bio.tools/paralyzer | SCR_001208 | PAR-CLIP data analyzer, PARalyzer (PAR-CLIP data analyzer) | 2026-09-19 12:49:36 | 7 | |||||
|
ProbRNA Resource Report Resource Website 1+ mentions |
ProbRNA (RRID:SCR_001288) | ProbRNA | software resource | Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data. | high-throughput sequencing, probe, rna structure, rna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:24376038 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:probrna, OMICS_02195 | https://bio.tools/probrna | SCR_001288 | 2026-09-19 12:49:38 | 1 | ||||||
|
VCFtools Resource Report Resource Website 1000+ mentions |
VCFtools (RRID:SCR_001235) | data management software, software application, software resource | Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API. | perl, genetic variation, variant call format, software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21653522 DOI:10.1093/bioinformatics/btr330 |
Free, Available for download, Freely available | OMICS_02105, SCR_012092, biotools:vcftools, OMICS_05112 | https://bio.tools/vcftools, https://sources.debian.org/src/vcftools/ | http://vcftools.sourceforge.net/ | SCR_001235 | Variant Call Format Tools | 2026-09-19 12:49:36 | 4555 | |||||
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Sequedex Resource Report Resource Website 1+ mentions |
Sequedex (RRID:SCR_001233) | Sequedex | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025.Software to classify the function and phylogeny of reads as short as 30 bp. It is flexible, which can utilize multiple data modules and downstream analysis scripts. It is fast, reading in signature lists of 5-500 million peptide signatures in 1-15 minutes, and subsequently processes genomic fragments at the rate of 6 Gbp/hr. It parallelizes without significant increase in memory requirements until I/O bound on multiple input files; parallelization works well on 64 processors. | phylogenetic, function, profile, metagenomics, synthetic, dna sequence, classification, java, linux, mac os, genomic analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Los Alamos National Laboratory |
PMID:22925230 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02110, biotools:sequedex | https://bio.tools/sequedex | SCR_001233 | 2026-09-19 12:49:36 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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