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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SOAP Resource Report Resource Website 100+ mentions |
SOAP (RRID:SCR_000689) | SOAP, | data processing software, software application, software resource | Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, next generation sequencing, alignment, short read, bio.tools |
lists: SOAPfusion lists: SOAPfuse lists: SOAPnuke lists: GapCloser is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: BGI; Shenzhen; China is parent organization of: SOAP3 is parent organization of: SOAPaligner/soap2 |
PMID:18227114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154652, biotools:soap | https://bio.tools/soap | SCR_000689 | SciCrunch Registry | SOAP: short oligonucleotide alignment program, Short Oligonucleotide Analysis Package | 2026-09-26 02:17:39 | 403 | |||||
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mlgt Resource Report Resource Website |
mlgt (RRID:SCR_001211) | mlgt | data processing software, software application, software resource | Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles. | roche, windows, os x, genotype, variant, allele, high throughput sequencing, locus, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Manchester; Manchester; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:mlgt, OMICS_02131, biotools:mlgt | https://bio.tools/mlgt, https://bio.tools/mlgt, https://bio.tools/mlgt | SCR_001211 | SciCrunch Registry | Multi-Locus Geno-Typing, mlgt: Multi-Locus Geno-Typing | 2026-09-26 02:17:40 | 0 | ||||||
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FASTX-Toolkit Resource Report Resource Website 1000+ mentions |
FASTX-Toolkit (RRID:SCR_005534) | data processing software, software application, software resource, software toolkit | Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. | Short reads, FASTA file, FASTQ file, preprocessing, command line tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
SCR_019035, SCR_015042, biotools:fastx-toolkit, OMICS_01045 | https://github.com/agordon/fastx_toolkit, https://bio.tools/fastx-toolkit | SCR_005534 | SciCrunch Registry | FASTQ/A short-reads pre-processing tools | 2026-09-26 02:17:43 | 2864 | ||||||||
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Mammalian Gene Collection Resource Report Resource Website 10+ mentions |
Mammalian Gene Collection (RRID:SCR_007024) | MGC | biomaterial supply resource, cell repository, material resource | NIH initiative project to provide full-length open reading frame (FL-ORF) clones for human, mouse, and rat genes, cow. MGC cDNA clones were obtained by screening of cDNA libraries, by transcript-specific RT-PCR cloning, and by DNA synthesis of cDNA inserts. All MGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of MGC project in March 2009, GenBank records of MGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which they have MGC clones will likely change in future, users planning to order MGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as the UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cell line, cdna, frozen, clone, vector, gene, open reading frame, sequence, expressed sequence tag, bio.tools, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: bio.tools is listed by: Debian is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: ATCC is related to: GenBank is related to: Invitrogen Clones is related to: Open Biosystems is related to: Zebrafish Gene Collection has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | biotools:mammalian_gene_collection, nif-0000-00195 | https://bio.tools/mammalian_gene_collection | SCR_007024 | SciCrunch Registry | Mammalian Gene Collection | 2026-09-26 02:17:45 | 46 | |||||
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SeqTrace Resource Report Resource Website 50+ mentions |
SeqTrace (RRID:SCR_005580) | SeqTrace | data processing software, software application, software resource | A software application for viewing and processing DNA sequencing chromatograms (trace files) that makes it easy to quickly generate high-quality finished sequences from a large number of trace files. SeqTrace can automatically identify, align, and compute consensus sequences from matching forward and reverse traces, filter low-quality base calls, and perform end trimming of finished sequences. The finished DNA sequences can then be exported to common sequence file formats, such as FASTA. SeqTrace also includes a full-featured trace file viewer and editor. You can view your sequencing chromatograms at a variety of scales and zoom levels, simultaneously view matching forward and reverse traces, edit the called bases, and export individual DNA sequences as well as forward/reverse alignments. SeqTrace supports popular trace file formats, including ABIF, SCF, and ZTR. | dna sequencing trace file, dna sequencing, trace file, trace, python, gtk, chromatogram, graphic, sequence analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code has parent organization: University of Colorado Boulder; Colorado; USA |
PMID:22942788 | GNU General Public License, v3 | OMICS_01021, biotools:seqtrace | https://bio.tools/seqtrace | SCR_005580 | SciCrunch Registry | Seqtrace - User-friendly software for viewing and processing DNA sequencing trace files | 2026-09-26 02:17:44 | 64 | |||||
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Sickle Resource Report Resource Website 1000+ mentions |
Sickle (RRID:SCR_006800) | Sickle | data processing software, software application, software resource | Software tool for windowed adaptive trimming for fastq files using quality. Supports quality values like Illumina, Solexa, and Sanger. Takes the quality values and slides a window across them whose length is 0.1 times the length of the read. | bio.tools, windowed, adaptive, trimming, FASTQ, quality, value, read |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | OMICS_01077, biotools:sickle, SCR_016901 | https://bio.tools/sickle, https://sources.debian.org/src/sickle/ | SCR_006800 | SciCrunch Registry | sickle - A windowed adaptive trimming tool for FASTQ files using quality | 2026-09-26 02:17:45 | 1664 | ||||||
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iDASH Resource Report Resource Website 1+ mentions |
iDASH (RRID:SCR_003524) | iDASH | data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications. | data sharing, computing, biomedical, behavior, molecular, phenotyping, kawasaki disease, hematologic medication, individualized intervention, physical activity, phenotype, data set, image, cyberinfrastructure, schema, domain model, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: DataCite is related to: National Centers for Biomedical Computing is related to: NIH Data Sharing Repositories is related to: National Centers for Biomedical Computing has parent organization: University of California at San Diego; California; USA has parent organization: University of California; California; USA |
NIH Roadmap for Bioinformatics and Computational Biology ; NHLBI U54 HL108460 |
PMID:22081224 | THIS RESOURCE IS NO LONGER IN SERVICE | https://api.datacite.org/dois?prefix=10.15147, biotools:iDASH, nif-0000-38239 | https://bio.tools/iDASH | SCR_003524 | SciCrunch Registry | iDASH Repository, Integrating Data for Analysis Anonymization and SHaring | 2026-09-26 02:17:42 | 2 | ||||
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biobambam Resource Report Resource Website 50+ mentions |
biobambam (RRID:SCR_003308) | data processing software, software application, software resource | Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1751-0473-9-13 | Free, Available for download, Freely available | biotools:biobambam, OMICS_04664 | https://bio.tools/biobambam, https://sources.debian.org/src/biobambam2/ | SCR_003308 | SciCrunch Registry | 2026-09-26 02:17:41 | 65 | |||||||
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Phenoscape Resource Report Resource Website 10+ mentions |
Phenoscape (RRID:SCR_003799) | Phenoscape | data or information resource, portal | Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions. | phenotype, bio.tools |
is listed by: Debian is listed by: bio.tools is parent organization of: Teleost Anatomy Ontology is parent organization of: Vertebrate Taxonomy Ontology is parent organization of: Phenoscape Knowledgebase |
NSF DBI-1062404; NSF DBI-1062542; NSF BDI-0641025; NSF EF-0905606; NSF EF-0423641 |
biotools:Phenoscape, nlx_158096 | https://bio.tools/Phenoscape | SCR_003799 | SciCrunch Registry | 2026-09-26 02:17:42 | 10 | |||||||
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RESCUE-ESE Resource Report Resource Website 50+ mentions |
RESCUE-ESE (RRID:SCR_008496) | data or information resource, database, organization portal, portal | Specific short oligonucleotide sequences that enhance pre-mRNA splicing when present in exons, termed exonic splicing enhancers (ESEs), play important roles in constitutive and alternative splicing (ESE References). A hybrid computational/experimental method, RESCUE-ESE, was recently developed for identifying sequences with ESE activity. In this approach, specific hexanucleotide sequences are identified as candidate ESEs on the basis that they have both significantly higher frequency of occurrence in exons than in introns and also significantly higher frequency in exons with weak (non-consensus) splice sites than in exons with strong (consensus) splice sites. Representative hexamers from ten different classes of candidate ESEs, together with 6 or 7 bases of flanking sequence context on each side, were introduced into a weak (poorly spliced) exon in a splicing reporter construct. These reporter minigenes were then transfected into cultured cells, where they are transcribed and spliced, and the relative level of inclusion of the test exon was assayed by quantitative (radio-labeled) RT-PCR. Point mutants of these sequences were also analyzed to confirm the precise motifs responsible for ESE activity. The RESCUE-ESE approach identified 238 hexamers as candidate ESEs using a large database of human genes of known exon-intron structure containing over 30,000 nonredudant exons. In more recent analyses by Yeo et al., the RESCUE-ESE approach was utilized to predict hexamers as candidate ESEs in other vertebrate genes, namely, Fugu rubipes, Zebrafish and Mouse. This allows the identification of motifs that are conserved in vertebrates. This web server allows a sequence to be checked for presence of these candidate ESE hexamers. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
biotools:rescue-ese, nif-0000-31403 | https://bio.tools/rescue-ese | http://genes.mit.edu/burgelab/rescue-ese/ | SCR_008496 | SciCrunch Registry | RESCUE-ESE | 2026-09-26 02:17:46 | 96 | |||||||
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HCLUST Resource Report Resource Website 1000+ mentions |
HCLUST (RRID:SCR_009154) | HCLUST | software application, software resource | Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, r, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:h-clust, SCR_009102, nlx_154195, nlx_154331 | https://bio.tools/h-clust | SCR_009154 | SciCrunch Registry | R/HCLUST | 2026-09-26 02:17:47 | 1460 | ||||||
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Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | data processing software, software application, software resource | Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows. | trimming, task, paired, end, single, data, next, generation, sequencing, filtering, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill |
BLE/BMELV Verbundprojekt ; BMBF |
PMID:24695404 DOI:10.1093/bioinformatics/btu170 |
biotools:trimmomatic, OMICS_01097 | https://omictools.com/trimmomatic-tool, https://bio.tools/trimmomatic, https://sources.debian.org/src/trimmomatic/ | SCR_011848 | SciCrunch Registry | Trimmomatic v 0.32 | 2026-09-26 02:17:48 | 23444 | |||||
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Open Babel Resource Report Resource Website 100+ mentions |
Open Babel (RRID:SCR_014920) | data analytics software, data processing software, software application, software resource | Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats. | toolbox, conversion, analysis, molecular model, chemistry, biochemistry, chemical file, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source | biotools:open_babel | https://bio.tools/open_babel | SCR_014920 | SciCrunch Registry | 2026-09-26 02:17:51 | 100 | ||||||||
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GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | data or information resource, dataset, portal, project portal | Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. | human, mouse, genome, annotation, sequence, gene features, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: ENCODE |
NHGRI 5U54HG004555; Wellcome Trust WT098051 |
PMID:22955987 | Free | biotools:GENCODE | https://bio.tools/GENCODE | SCR_014966 | SciCrunch Registry | ENCODE | 2026-09-26 02:17:51 | 8811 | |||||
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | data processing software, image analysis software, software application, software resource | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | SciCrunch Registry | outfi | 2026-09-26 02:17:52 | 15 | ||||||
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xia2 pipeline Resource Report Resource Website 10+ mentions |
xia2 pipeline (RRID:SCR_015746) | data processing software, software application, software resource | Data processing software that performs X-ray diffraction data processing. It handles multi-pass, multi-wavelength data sets and supports remote access to synchrotron facilities. | xray, diffraction, data processing, synchrotron, mmulti-pass, multi-wavelength, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:23793152 | Open Source, Available for download | biotools:xia2 | https://bio.tools/xia2 | SCR_015746 | SciCrunch Registry | 2026-09-26 02:17:51 | 34 | |||||||
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rnaQUAST Resource Report Resource Website 1+ mentions |
rnaQUAST (RRID:SCR_016994) | data processing software, software application, software resource | Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software. | evaluation, quality, RNA-Seq, assembly, data, transcriptome, assembler, reference, genome, gene, database, raw, read, , bio.tools |
uses: BUSCO is listed by: Debian is listed by: bio.tools is related to: rnaSPAdes is related to: Python Programming Language is related to: SPAdes |
EMC Research and Development Department ; St. Petersburg State University ; Russia |
PMID:27153654 | Free, Available for download, Freely available | biotools:rnaQUASt | https://bio.tools/rnaQUAST | SCR_016994 | SciCrunch Registry | 2026-09-26 02:17:53 | 4 | ||||||
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Metabolomics Workbench Resource Report Resource Website 500+ mentions |
Metabolomics Workbench (RRID:SCR_013794) | MetWB | data or information resource, data repository, service resource, storage service resource | Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops. | repository, metabolomics, database, funding, training, protocol, bio.tools, FASEB list, DRKB |
is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases lists: NIH Metabolomics program lists: MetaCore lists: JMP lists: STATISTICA lists: Spotfire lists: Coordination of Standards in Metabolomics lists: MetaboLights lists: MetabolomeXchange lists: Metabolomics Society lists: Birmingham Metabolite Library lists: Glycan Mass Spectral Database (GMDB) lists: Mass Spectral Library lists: mzCloud lists: MetabolomeExpress lists: Spectral Database System (SDBS) lists: CTSgetR lists: Hierarchical Clustering lists: imDEV lists: Linear Discriminant Analysis lists: Principal Components Analysis lists: mwtabR lists: 3Omics lists: ACD/ NMR Processor lists: NIST Mass Spectrometry Data Center lists: Chemical Translation Service lists: Chenomx NMR Suite lists: DeviumWeb lists: MBRole lists: MetaMapR lists: MetaP lists: Metscape lists: SIMCA lists: TeachingDemos is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is listed by: re3data.org is listed by: DataCite has parent organization: University of California; California; USA is parent organization of: Metabolomics Workbench Metabolite Database |
NIDDK DK141185; NIH |
Free, Freely available | biotools:Metabolomics_Workbench, r3d100012314 | https://bio.tools/Metabolomics_Workbench, https://api.datacite.org/dois?prefix=10.21228 | SCR_013794 | SciCrunch Registry | Metabolomics Workbench, MetWB, UCSD Metabolomics Workbench, Metabolomics Workbench (MetWB) | 2026-09-26 02:15:20 | 666 | |||||
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Membrane Protein Explorer Resource Report Resource Website 10+ mentions |
Membrane Protein Explorer (RRID:SCR_014077) | MPEx | data analysis software, data processing software, software application, software resource | Software which predicts topology and other features of membrane proteins through hydropathy plots based on thermodynamic and biological principles. This version of MPEx uses two types of hydropathy scales: Experiment-based whole-residue partitioning scales and experiment-based biological partitioning scales. The whole-residue partitioning scales predict the transmembrane (TM) segments of membrane proteins of known structure. The biological scale utilizes current knowledge of the code the Sec61 translocon to identify TM segments. MPEx is a Java program (not a Java applet) deployed using Java Web Start, which is part of the Java Runtime Environment. | membrane protein, hydropathy plot, topology, software, java, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Irvine; California; USA |
PMID:19785006 | Available to the research community, Requires version 7 or higher of Java Runtime Environment | biotools:mpex | https://bio.tools/mpex | SCR_014077 | SciCrunch Registry | Membrane Protein Explorer (MPEx) | 2026-09-26 02:15:21 | 34 | |||||
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Buccaneer Resource Report Resource Website 100+ mentions |
Buccaneer (RRID:SCR_014221) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. The target distributions are generated by a simulation calculation using a known reference structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved work structure. For almost all cases, a single reference structure can be used, with modifications automatically applied to the reference structure to match its features to the work structure. | statistical chain tracing, alpha carbon position, sequence analysis software, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:16929101 | biotools:buccaneer | https://bio.tools/buccaneer | SCR_014221 | SciCrunch Registry | buccaneer - Statistical protein chain tracing | 2026-09-26 02:15:23 | 335 |
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