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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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GNUMAP Resource Report Resource Website 1+ mentions |
GNUMAP (RRID:SCR_005482) | GNUMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A software program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. By using the posterior probability of mapping a given read to a specific genomic loation, we are able to account for repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily- available programs. Several benchmark data sets were created with spiked-in duplicate regions, and GNUMAP was able to more accurately account for these duplicate regions. | next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00664, biotools:gnumap | https://bio.tools/gnumap | SCR_005482 | SciCrunch Registry | Genomic Next-generation Universal MAPper | 2026-10-10 12:37:19 | 7 | ||||||
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SAMStat Resource Report Resource Website 10+ mentions |
SAMStat (RRID:SCR_005432) | SAMStat | software resource | C software program for displaying sequence statistics for next generation sequencing. Works with large fasta, fastq and SAM/BAM files. | sequence statistic, c, next generation sequencing, fasta file, fastq file, sam file, bam file, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: RIKEN Yokohama Institute; Kanagawa; Japan |
PMID:21088025 | Acknowledgement requested | biotools:samstat, OMICS_01073 | https://bio.tools/samstat | SCR_005432 | SciCrunch Registry | 2026-10-10 12:37:17 | 39 | ||||||
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SolexaQA Resource Report Resource Website 100+ mentions |
SolexaQA (RRID:SCR_005421) | SolexaQA | data analysis software, data processing software, data visualization software, sequence analysis software, software application, software resource | Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20875133 | Acknowledgement requested | biotools:solexaqa, OMICS_01078 | https://bio.tools/solexaqa | SCR_005421 | SciCrunch Registry | 2026-10-10 12:37:14 | 297 | ||||||
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MethylViewer Resource Report Resource Website 1+ mentions |
MethylViewer (RRID:SCR_005448) | MethylViewer | software resource | A simple integrated software tool for handling MAP (methyltransferase accessibility protocol) and MAP-IT (MAP individual templates) footprinting projects. It can process sequence data (*.txt, *.ab1 and *.scf) derived from the use of up to four different DNA methyltransferases. | primer design, bisulfite sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Leeds; West Yorkshire; United Kingdom |
PMID:20959287 | OMICS_00608, biotools:methylviewer | https://bio.tools/methylviewer | SCR_005448 | SciCrunch Registry | 2026-10-10 12:37:14 | 2 | |||||||
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HiCUP Resource Report Resource Website 100+ mentions |
HiCUP (RRID:SCR_005569) | HiCUP | software resource | A tool for mapping and performing quality control on Hi-C data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
OMICS_00523, biotools:hicup | https://bio.tools/hicup | SCR_005569 | SciCrunch Registry | Hi-C User Pipeline | 2026-10-10 12:37:08 | 317 | |||||||
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Bis-SNP Resource Report Resource Website 50+ mentions |
Bis-SNP (RRID:SCR_005439) | Bis-SNP | software resource | A software package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. It contains the following key features: * Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.); * Work for single end and paired-end data; * Accurtae variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing; * Based on Java map-reduce framework, allow multi-thread computing. Cross-platform; * Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysis, simplified bedGraph, wig and bed format for visualization in UCSC genome broswer and IGV browser. BisSNP uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:22784381 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:bis-snp, OMICS_00591 | https://bio.tools/bis-snp | SCR_005439 | SciCrunch Registry | Bis-SNP - A bisulfite space genotyper & methylation caller, Bis-SNP - A bisulfite space genotyper and methylation caller | 2026-10-10 12:37:18 | 50 | |||||
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DistMap Resource Report Resource Website 10+ mentions |
DistMap (RRID:SCR_005473) | DistMap | software resource | A user-friendly software pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster. It is designed to be easily implemented by researchers who do not have expert knowledge of bioinformatics. As it does not have any dependencies, it provides full flexibility and control to the user. The user can use any version of a compatible mapper and any reference genome assembly. There is no need to maintain the mapper, reference or DistMap source code on each of the slaves (nodes) in the Hadoop cluster, making maintenance extremely easy. | mapreduce/hadoop, command line, hadoop cluster, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Veterinary Medicine Vienna; Vienna; Austria has parent organization: Google Code |
PMID:24009693 | GNU General Public License, v3 | OMICS_00660, biotools:distmap | https://bio.tools/distmap | SCR_005473 | SciCrunch Registry | 2026-10-10 12:37:42 | 23 | ||||||
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Stampy Resource Report Resource Website 100+ mentions |
Stampy (RRID:SCR_005504) | Stampy | software resource | A software package for the mapping of short reads from illumina sequencing machines onto a reference genome. It''s recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: * Maps single, paired-end and mate pair Illumina reads to a reference genome * Fast: about 20 Gbase per hour in hybrid mode (using BWA) * Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome * High sensitivity for indels and divergent reads, up to 10-15% * Low mapping bias for reads with SNPs * Well calibrated mapping quality scores * Input: Fastq and Fasta; gzipped or plain * Output: SAM, Maq''s map file * Optionally calculates per-base alignment posteriors * Optionally processes part of the input * Handles reads of up to 4500 bases | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:20980556 | OMICS_00691, biotools:stampy | https://bio.tools/stampy | SCR_005504 | SciCrunch Registry | 2026-10-10 12:37:44 | 184 | |||||||
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Scalable Nucleotide Alignment Program Resource Report Resource Website 100+ mentions |
Scalable Nucleotide Alignment Program (RRID:SCR_005501) | SNAP | software resource | A sequence aligner software program that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing. | windows, linux, os x |
is listed by: OMICtools is listed by: Debian has parent organization: University of California at Berkeley; Berkeley; USA |
Apache License, 2, Acknowledgement requested | OMICS_00687 | https://sources.debian.org/src/snap-aligner/ | SCR_005501 | SciCrunch Registry | SNAP - Scalable Nucleotide Alignment Program | 2026-10-10 12:37:20 | 124 | ||||||
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NGSView Resource Report Resource Website 1+ mentions |
NGSView (RRID:SCR_005637) | NGSView | software resource | A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. | next-generation sequence, alignment, edit, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Acknowledgement requested | biotools:ngsview, OMICS_00891 | https://bio.tools/ngsview | SCR_005637 | SciCrunch Registry | 2026-10-10 12:37:18 | 2 | |||||||
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Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | data or information resource, database, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | SciCrunch Registry | Sybil: Web-based software for comparative genomics | 2026-10-10 12:37:22 | 37 | ||||||
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OLego Resource Report Resource Website 10+ mentions |
OLego (RRID:SCR_005811) | OLego | software resource | A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
biotools:olego, OMICS_01244 | https://bio.tools/olego | SCR_005811 | SciCrunch Registry | 2026-10-10 12:37:12 | 15 | ||||||||
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PePr Resource Report Resource Website 50+ mentions |
PePr (RRID:SCR_005759) | PePr | software resource | A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions. | python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24894502 | GNU General Public License, v3 | OMICS_04058, biotools:pepr | https://bio.tools/pepr | SCR_005759 | SciCrunch Registry | pepr-chip-seq, Peak Prioritization Pipeline, pepr-chip-seq: A ChIP-Seq analyzing program for biological replicates | 2026-10-10 12:37:27 | 55 | |||||
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GraphProt Resource Report Resource Website 10+ mentions |
GraphProt (RRID:SCR_005842) | GraphProt | software resource | Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete. | sequence-binding preference, structure-binding preference, rna-binding protein, high-throughput sequencing, clip-seq, rnacompete, rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
PMID:24451197 | Free, Public | OMICS_02252, biotools:graphprot | https://bio.tools/graphprot | SCR_005842 | SciCrunch Registry | 2026-10-10 12:37:29 | 39 | ||||||
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CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | SciCrunch Registry | 2026-10-10 12:37:27 | 20 | ||||||
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Europe PubMed Central Resource Report Resource Website 500+ mentions |
Europe PubMed Central (RRID:SCR_005901) | Europe PMC, UKPMC | bibliography, data access protocol, data or information resource, database, software resource, web service | Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts. | biomedical, literature, publication, health, life science, patent, clinical guideline, grant, text mining, author identification, archiving, open access, gold standard, bio.tools, bio.tools, FASEB list |
uses: EvidenceFinder uses: BioLexicon is listed by: FORCE11 is listed by: Debian is listed by: bio.tools is related to: PubMed is related to: PubMed Central is related to: AGRICOLA is related to: ORCID - Open Researcher and Contributor ID is related to: EvidenceFinder has parent organization: European Bioinformatics Institute has parent organization: Mimas has parent organization: National Centre for Text Mining is parent organization of: EvidenceFinder |
Wellcome Trust WT098231 | PMID:21062818 | Free, The community can contribute to this resource | nlx_149472, biotools:europe_pmc, biotools:ukpmc | https://bio.tools/ukpmc, https://bio.tools/europe_pmc | http://ukpmc.ac.uk/ | SCR_005901 | SciCrunch Registry | UK PubMed Central | 2026-10-10 12:37:14 | 517 | |||
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Cascade Resource Report Resource Website 50+ mentions |
Cascade (RRID:SCR_005861) | Cascade | software resource | R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, windows, gene expression, perturbation, network, diffusion, signal, temporal gene network, gene regulatory network, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Strasbourg; Strasbourg; France |
PMID:24307703 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02249, biotools:cascade | http://www-math.u-strasbg.fr/genpred/spip.php?rubrique4, https://bio.tools/cascade | SCR_005861 | SciCrunch Registry | 2026-10-10 12:37:13 | 92 | ||||||
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BiNGO: A Biological Networks Gene Ontology tool Resource Report Resource Website 500+ mentions |
BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) | BiNGO | software resource | The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, ontology, statistical analysis, term enrichment, biological network, plugin, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Cytoscape has parent organization: Ghent University; Ghent; Belgium |
PMID:15972284 | Open unspecified license - Free for academic use | nlx_149196, biotools:bingo | https://bio.tools/bingo | SCR_005736 | SciCrunch Registry | Biological Networks Gene Ontology | 2026-10-10 12:37:19 | 806 | |||||
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959 Nematode Genomes Resource Report Resource Website 1+ mentions |
959 Nematode Genomes (RRID:SCR_006068) | NematodeGenomes | data or information resource, narrative resource, wiki | A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs. | nematode, genome, genome sequencing, transcriptome sequencing, blast, genomics, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: nematodes.org has parent organization: University of Edinburgh; Scotland; United Kingdom |
NERC | PMID:22058131 | nlx_151473, biotools:959_nematode_genomes | https://bio.tools/959_nematode_genomes | SCR_006068 | SciCrunch Registry | NematodeGenomes | 2026-10-10 12:37:34 | 2 | |||||
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MMMDB - Mouse Multiple tissue Metabolome DataBase Resource Report Resource Website 1+ mentions |
MMMDB - Mouse Multiple tissue Metabolome DataBase (RRID:SCR_006064) | MMMDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided. | metabolite, metabolome, cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, plasma, metabolomic pathway, capillary electropherograms time-of-flight mass spectrometry, electropherogram, mass spectrometry, annotation, isotope, fragment, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:22139941 | Free | nlx_151467, biotools:mmmdb | https://bio.tools/mmmdb | SCR_006064 | SciCrunch Registry | Mouse Multiple tissue Metabolome DataBase | 2026-10-10 12:37:24 | 1 |
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