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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ray Resource Report Resource Website 1+ mentions |
Ray (RRID:SCR_001916) | Ray | software resource | Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. | mpi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20958248 DOI:10.1089/cmb.2009.0238 |
Free, Available for download, Freely available | OMICS_00027, biotools:ray | https://bio.tools/ray, https://sources.debian.org/src/ray/ | SCR_001916 | SciCrunch Registry | Ray - a de novo assembler using MPI 2.2, Ray - Parallel genome assemblies for parallel DNA sequencing | 2026-10-24 12:44:38 | 1 | |||||
|
openADAM Resource Report Resource Website |
openADAM (RRID:SCR_002018) | openADAM | data management software, software application, software resource | A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms. | php, perl, front end, affymetrix genechip mapping array, affymetrix genome-wide human snp array, data management, affymetrix, snp, genome-wide association |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19117518 | Free, Available for download, Freely available | OMICS_01921 | SCR_002018 | SciCrunch Registry | 2026-10-24 12:44:39 | 0 | |||||||
|
DMET-Analyzer Resource Report Resource Website 1+ mentions |
DMET-Analyzer (RRID:SCR_002030) | DMET-Analyzer | software resource | Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way. | drug, metabolism, enzyme, transporter, affymetrix, variation, genome, clinical, affymetrix dmet, single nucleotide polymorphism, annotation, analysis, pharmacogenomic, pathway |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23035929 | Free, Available for download, Freely available | OMICS_01920 | SCR_002030 | SciCrunch Registry | DMETANALYZER, DMETANALYZER - A tool for supporting pharmacogenomics data analysis | 2026-10-24 12:44:39 | 1 | ||||||
|
SNVer Resource Report Resource Website 50+ mentions |
SNVer (RRID:SCR_002061) | data analysis software, data processing software, software application, software resource | Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data. | statistical analysis software, sequencing, dna, whole-exome, whole-genome, variant, bio.tools |
lists: SAMTOOLS is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:21813454 | Free, Available for download, Freely available | OMICS_00076, biotools:snver | https://sourceforge.net/projects/snver/, https://bio.tools/snver | SCR_002061 | SciCrunch Registry | 2026-10-24 12:44:39 | 52 | |||||||
|
Cake Resource Report Resource Website 10+ mentions |
Cake (RRID:SCR_002133) | software resource | A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. | standalone software, unix/linux, mac os x, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23803469 | Free, Available for download, Freely available | OMICS_03613, biotools:cake | https://bio.tools/cake | SCR_002133 | SciCrunch Registry | 2026-10-24 12:44:43 | 11 | |||||||
|
Matchprot Resource Report Resource Website |
Matchprot (RRID:SCR_002163) | software resource | A pairwise protein structure alignment software. | standalone software, c |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17338826 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03666 | SCR_002163 | SciCrunch Registry | 2026-10-24 12:44:40 | 0 | ||||||||
|
Software Ontology Resource Report Resource Website 1+ mentions |
Software Ontology (RRID:SCR_003493) | SWO | controlled vocabulary, data or information resource, ontology | An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to). | owl, software, provenance, version, ontology |
is listed by: BioPortal is listed by: OBO is listed by: SourceForge is related to: Information Artifact Ontology has parent organization: European Bioinformatics Institute has parent organization: University of Manchester; Manchester; United Kingdom |
JISC | The community can contribute to this resource | nlx_157591 | http://www.ebi.ac.uk/efo/swo, http://purl.bioontology.org/ontology/SWO, http://theswo.svn.sourceforge.net/viewvc/theswo/trunk/src/release/swoinowl/swo_merged/swo_merged.owl | SCR_003493 | SciCrunch Registry | 2026-10-24 12:45:00 | 2 | ||||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | SciCrunch Registry | Genome Expression Pathway Analysis Tool | 2026-10-24 12:45:00 | 2 | ||||||
|
Jmol Resource Report Resource Website 100+ mentions |
Jmol (RRID:SCR_003796) | Jmol | d visualization software, software application, software resource, standalone software | An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component. | chemical, crystal, material, biomolecule, java |
is used by: Glyco3D is listed by: SoftCite has parent organization: SourceForge |
PMID:28472503 PMID:28316648 |
GNU Lesser General Public License, Acknowledgement requested | nlx_158093 | SCR_003796 | SciCrunch Registry | Jmol: an open-source Java viewer for chemical structures in 3D | 2026-10-24 12:45:02 | 245 | ||||||
|
InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | SciCrunch Registry | 2026-10-24 12:45:08 | 0 | ||||||
|
CB-Commander Resource Report Resource Website |
CB-Commander (RRID:SCR_004237) | CB-Commander | software resource | A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline. | java, java swing, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
GNU General Public License, v2 | OMICS_01534 | http://sourceforge.net/projects/cb-commander/ | SCR_004237 | SciCrunch Registry | 2026-10-24 12:45:09 | 0 | |||||||
|
mrFAST Resource Report Resource Website 10+ mentions |
mrFAST (RRID:SCR_005487) | mrFAST | software resource | Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SPLITREAD has parent organization: SourceForge |
PMID:19718026 | biotools:mrfast, OMICS_00671 | https://bio.tools/mrfast | SCR_005487 | SciCrunch Registry | mrFAST - Micro Read Fast Alignment Search Tool, Micro Read Fast Alignment Search Tool | 2026-10-24 12:45:27 | 16 | ||||||
|
CUSHAW2-GPU Resource Report Resource Website |
CUSHAW2-GPU (RRID:SCR_005480) | CUSHAW2-GPU | software resource | Software program (based on CUSHAW2) designed and optimized for Kepler-based GPUs, but still workable on earlier-generation Fermi-based ones. | c++, genome, alignment |
is listed by: OMICtools is related to: CUSHAW has parent organization: SourceForge |
Apache License | OMICS_00659 | SCR_005480 | SciCrunch Registry | 2026-10-24 12:45:27 | 0 | ||||||||
|
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 | 2026-10-24 12:45:26 | 297 | ||||||
|
CUSHAW Resource Report Resource Website 1+ mentions |
CUSHAW (RRID:SCR_005479) | CUSHAW | software resource | Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome. | next-generation sequencing, read alignment, genome, alignment |
is listed by: OMICtools is related to: CUSHAW2-GPU has parent organization: Johannes Gutenberg University Mainz; Rhineland-Palatinate; Germany has parent organization: SourceForge |
PMID:22576173 PMID:24466273 |
OMICS_00658 | SCR_005479 | SciCrunch Registry | CUSHAW2, CUSHAW3 | 2026-10-24 12:45:27 | 2 | |||||||
|
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 | 2026-10-24 12:45:30 | 2 | |||||||
|
SAMtools Text Alignment Viewer Resource Report Resource Website 1+ mentions |
SAMtools Text Alignment Viewer (RRID:SCR_005611) | SAMtools tview | software resource | Text alignment viewer software based on the GNU ncurses library that works with short indels and shows MAQ consensus. It uses different colors to display mapping quality or base quality, subjected to users' choice. | text alignment, viewer, maq consensus, indel |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00893 | SCR_005611 | SciCrunch Registry | Text Alignment Viewer | 2026-10-24 12:45:29 | 1 | ||||||||
|
Manatee Resource Report Resource Website 50+ mentions |
Manatee (RRID:SCR_005685) | Manatee | software resource | Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris | gene, genome, annotation, ontology or annotation browser, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: SourceForge |
Open unspecified license - Free for academic use | nlx_149128 | SCR_005685 | SciCrunch Registry | 2026-10-24 12:45:30 | 64 | ||||||||
|
cancergrid-tma Resource Report Resource Website |
cancergrid-tma (RRID:SCR_005595) | cancergrid-tma | software resource | A web-based application for the management and storage of tissue microarray (TMA) images and the associated metadata. The application enables the user to navigate a grid of TMA core images within a slide, zoom and pan around an image, and enter a score constrained to a specific scoring system. The submitted scores are scored in the eXist open source database, in an XML format, which is compatible with existing TMA standards, and thus allow the data to be archived and re-used in future analysis. | tissue microarray, image |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00816 | SCR_005595 | SciCrunch Registry | Cancergrid Image Scorer | 2026-10-24 12:45:29 | 0 | ||||||||
|
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 | 2026-10-24 12:45:29 | 37 |
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