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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GASiC Resource Report Resource Website 1+ mentions |
GASiC (RRID:SCR_006765) | GASiC | software resource | A method to correct read alignment results for the ambiguities imposed by similarities of genomes. | metagenome, genome, sequence, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:22941661 DOI:10.1093/nar/gks803 |
BSD License | OMICS_01437 | https://sources.debian.org/src/gasic/ | SCR_006765 | SciCrunch Registry | GASiC - Genome Abundance Similarity Correction, Genome Abundance Similarity Correction | 2026-11-07 11:56:01 | 3 | |||||
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Next-gen Sequencing Scaffolding Tool Resource Report Resource Website |
Next-gen Sequencing Scaffolding Tool (RRID:SCR_006762) | Next-gen Sequencing Scaffolding Tool | software resource | Software that implements a greedy algorithm and uses graph theory to link and orient assembled existing contigs quickly and accurately using mate pair information. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00040 | SCR_006762 | SciCrunch Registry | 2026-11-07 11:56:01 | 0 | ||||||||||
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QUASR Resource Report Resource Website 100+ mentions |
QUASR (RRID:SCR_006820) | QUASR | software resource | A lightweight software pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset. Functions include: duplicate removal, demultiplexing, primer-removal, quality-assurance (QA) graphing, quality control (QC), consensus-generation, minority-variant determination, minority-variant graphing. | next generation sequencing, python3, java |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01072 | SCR_006820 | SciCrunch Registry | QUASR - Cross-platform NGS processing and analysis pipeline in Python | 2026-11-07 11:56:15 | 219 | |||||||
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simhtsd Resource Report Resource Website |
simhtsd (RRID:SCR_006822) | simhtsd | software resource | Software that given a reference sequence, will create a large set of short nucleotide reads, simulating the output from today''s high-throughput DNA sequencers, such as the Illumina Genome Analyzer II. | command-line, perl |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2, v3 | OMICS_00256 | SCR_006822 | SciCrunch Registry | Simulate High-Throughput Sequencing Data | 2026-11-07 11:56:03 | 0 | |||||||
|
bioNerDS Resource Report Resource Website 1+ mentions |
bioNerDS (RRID:SCR_006784) | bioNerDS | data or information resource, data set, software application, software resource, source code, text-mining software | A named entity recognizer for the recovery of bioinformatics databases and software from primary literature. The entity recognizer achieved an F-measure of between 63% and 91% on different datasets (63%78% at the document level). Results from full-text literature analysis for both Genome Biology and BMC Bioinformatics journals are available as well as a full list of references and links for the various major resources mentioned. Data generated data can be used for exploration of bioinformatics database and software usage. This tool makes heavy use of GATE (version 6.1). It can be run in sandbox mode, which means a installation of GATE is not a prerequisite, but you will instead need to point the config to a unzipped gate_plugins directory instead (located in the bin/BMC_Files directory). | literature mining, bioinformatics, database, software, resource |
has parent organization: SourceForge has parent organization: University of Manchester; Manchester; United Kingdom |
BBSRC | PMID:23768135 | Open-source license, Acknowledgement requested, Source code, Simplified BSD License, All included libraries retain their own respective licenses. Some source code from other projects has been used/adapted for inclusion in this project (e.g., LINNAEUS, JCommander, JOrtho, GATE and Snowball). Attribution for these remains with the original respective authors, And is distributed in accordance with their own licenses. | nlx_152793 | SCR_006784 | SciCrunch Registry | Bioinformatics Named Entity Recognizer for Databases and Software, Bioinformatics Named Entity Recogniser for Databases and Software | 2026-11-07 11:56:17 | 3 | |||||
|
Virmid Resource Report Resource Website 1+ mentions |
Virmid (RRID:SCR_006780) | Virmid | software resource | A Java based variant caller designed for disease-control matched samples. Virmid is also specialized for identifying potential within individual contamination where the disease sample cannot be purified enough. While the SNP calling rate is severely compromised with this heterogeneity, Virmid can uncover SNPs with low allele frequency by considering the level of contamination (alpha). The important features of Virmid are: * Estimation of accurate proporation of control sample in a (mixed) disease sample * Improved SNP and somatic mutation calling with regard to the estimated proportion | somatic mutation, sample impurity, java, snp, variant, disease, control |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at San Diego; California; USA |
PMID:23987214 | OMICS_00095 | SCR_006780 | SciCrunch Registry | Virtual Microdissection for SNP calling | 2026-11-07 11:56:02 | 6 | |||||||
|
BIGpre Resource Report Resource Website |
BIGpre (RRID:SCR_006781) | BIGpre | software resource | A quality assessment software package for next-genomics sequencing data. | next generation sequencing, genomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22289480 | GNU General Public License, v3 | biotools:bigpre, OMICS_01035 | https://bio.tools/bigpre | SCR_006781 | SciCrunch Registry | 2026-11-07 11:56:01 | 0 | ||||||
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TaxoAssignement Resource Report Resource Website 100+ mentions |
TaxoAssignement (RRID:SCR_006814) | TANGO | software resource | Software tool for the taxonomic assignment of Next Generation Sequencing reads using multiple reference taxonomy. | next generation sequencing, taxonomy, perl |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Polytechnic University of Catalonia; Barcelona; Spain |
MIT License | OMICS_01439 | http://www.cs.upc.edu/~valiente/tango/ | SCR_006814 | SciCrunch Registry | Taxonomic assignment of sequences, TANGO: Taxonomic Assignment in Metagenomics | 2026-11-07 11:56:15 | 246 | ||||||
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DeconSeq Resource Report Resource Website 100+ mentions |
DeconSeq (RRID:SCR_007006) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface. The user can upload FASTA or FASTQ files and select the databases used for contamination screening, including seven human genomes, bacterial genomes, and viral genomes. The user can set the thresholds interactivly and see the results directly using the functionality of the graphical interface. The results can be downloaded in joined or separated files in different formats. The coverage-identity plots provide additional information that can guide the selections of the thresholds using color coded points and connecting lines. | microbiome, sequence analysis, genomic, metagenomic, datasets, contamination, decontamination, FASEB list |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: SourceForge |
Available for download | OMICS_01418 | SCR_007006 | SciCrunch Registry | DECONtamination of SEQuence data, decontamination of sequence data | 2026-11-07 11:56:19 | 213 | ||||||||
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Monte Carlo eXtreme Resource Report Resource Website 1+ mentions |
Monte Carlo eXtreme (RRID:SCR_007001) | MCX | simulation software, software application, software resource | A Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470. | c, console (text based), macos, microsoft, modeling, monte carlo, optical imaging, other programming language, posix/unix-like, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155817 | http://www.nitrc.org/projects/mcextreme | SCR_007001 | SciCrunch Registry | Monte Carlo eXtreme (MCX) | 2026-11-07 11:56:17 | 2 | ||||||
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RUbioSeq Resource Report Resource Website 10+ mentions |
RUbioSeq (RRID:SCR_002508) | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments. | resequencing analysis, exome variant detection, pipeline, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
BLUEPRINT Consortium FP7/2007-2013 282510; Spanish Ministry of Economy and Competitiveness BIO2007-666855 |
PMID:23630175 | Free, Available for download | biotools:rubioseq, OMICS_00072 | https://sourceforge.net/projects/rubioseq/files/, https://bio.tools/rubioseq | SCR_002508 | SciCrunch Registry | RUbioSeq+ | 2026-11-07 11:54:57 | 12 | |||||
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Batch Oligo Selection Script Resource Report Resource Website |
Batch Oligo Selection Script (RRID:SCR_002808) | BOSS | software resource | Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps. | primer, pcr, oligo, contig, scaffold, command-line, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Freely available, Available for download | OMICS_02334 | SCR_002808 | SciCrunch Registry | 2026-11-07 11:54:46 | 0 | ||||||||
|
MIPE Resource Report Resource Website 10+ mentions |
MIPE (RRID:SCR_003065) | data or information resource, interchange format, narrative resource, software resource, standard specification | A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file. | standalone software, pcr, xml, data storage, data exchange |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02358 | http://mipe.sourceforge.net/, https://sources.debian.org/src/mipe/ | SCR_003065 | SciCrunch Registry | Minimal Information for PCR Experiments | 2026-11-07 11:55:02 | 32 | |||||||
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mrsFAST Resource Report Resource Website 10+ mentions |
mrsFAST (RRID:SCR_003128) | mrsFAST | software resource | A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter) | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
PMID:20676076 | Free, Available for download, Freely available | biotools:mrsfast, nlx_156780 | https://bio.tools/mrsfast | SCR_003128 | SciCrunch Registry | mrsFAST: micro-read substitution-only Fast Alignment Search Tool, micro-read substitution-only Fast Alignment Search Tool | 2026-11-07 11:55:09 | 22 | |||||
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SobekCM Resource Report Resource Website |
SobekCM (RRID:SCR_003225) | SobekCM | software resource | Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories. | archiving, resource management, metadata standard, ontology, data repository, research object, c#, windows |
is listed by: FORCE11 has parent organization: University of Florida; Florida; USA has parent organization: Google Code has parent organization: SourceForge |
NEH ; NSF ; NHPRC ; IMLS |
Free, Available for download, Freely available | nlx_157266 | SCR_003225 | SciCrunch Registry | SobekCM Digital Repository Software, SobekCM : Digital Content Management System, SobekCM Digital Repository | 2026-11-07 11:55:04 | 0 | ||||||
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Metabolomics Standards Initiative Resource Report Resource Website 10+ mentions |
Metabolomics Standards Initiative (RRID:SCR_003246) | MSI | controlled vocabulary, data or information resource, knowledge environment, narrative resource, ontology, standard specification | Oversight Committee appointed to monitor, coordinate and review the efforts of working groups (WG) in specialist areas (Biological context metadata WG, Chemical analysis WG, Data processing WG, Ontology WG, Exchange format WG) that will examine standardization and make recommendations. | metabolomics, biological context, metadata, chemical analysis, data processing, exchange format |
is related to: NMR-Instrument Component of Metabolomics Investigations Ontology has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_157308 | https://github.com/MSI-Metabolomics-Standards-Initiative/CIMR | SCR_003246 | SciCrunch Registry | 2026-11-07 11:55:04 | 15 | |||||||
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SpliCQ Resource Report Resource Website |
SpliCQ (RRID:SCR_003266) | SpliCQ | software resource | A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01341 | SCR_003266 | SciCrunch Registry | 2026-11-07 11:55:04 | 0 | ||||||||
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ORFprimer Resource Report Resource Website 1+ mentions |
ORFprimer (RRID:SCR_003269) | ORFprimer | software resource | An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number. | java, java swing, open reading frame, protein, high throughput sequencing, primer, primer design, pcr, pcr primer design |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02331 | SCR_003269 | SciCrunch Registry | ORFprimer - primer design for ORFs | 2026-11-07 11:54:59 | 1 | |||||||
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Gemi Resource Report Resource Website 10+ mentions |
Gemi (RRID:SCR_003211) | Gemi | software resource | Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences. | polymerase chain reaction, primer, pcr primer design, pcr primer, dna sequence, rna sequence, c#, .net/mono, windows, probe, multiple aligned sequence |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23316117 | Free, Available for download, Freely available | OMICS_02332 | SCR_003211 | SciCrunch Registry | Gemi - PCR oligos / primers design from multiple sequence alignments | 2026-11-07 11:55:11 | 13 | ||||||
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Vertebrate Trait Ontology Resource Report Resource Website |
Vertebrate Trait Ontology (RRID:SCR_003214) | VT | controlled vocabulary, data or information resource, ontology | A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. | trait, morphology, physiology, development, obo |
is listed by: BioPortal is related to: monarch-ontologies is related to: Rat Genome Database (RGD) is related to: Animal QTLdb is related to: Mouse Phenome Database (MPD) has parent organization: SourceForge |
PMID:23937709 | Free, Available for download, Freely available | nlx_156940 | SCR_003214 | SciCrunch Registry | VT Ontology | 2026-11-07 11:54:52 | 0 |
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