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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | |||||||
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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 | |||||||
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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 | ||||||
|
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 | ||||||||
|
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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Multiscale Object Orientation Simulation Environment Resource Report Resource Website 100+ mentions |
Multiscale Object Orientation Simulation Environment (RRID:SCR_008031) | simulation software, software application, software resource | MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. it is backwards-compatible with GENESIS, and forward compatible with Python and XML-based model definition standards like SBML and MorphML. MOOSE is coordinating with the GENESIS-3 project towards the goals of developing educational resources for modeling. MOOSE is open source software, licensed under the LGPL (Lesser GNU Public License). It has absolutely no warranty. Sponsors: - National Center of Biological Sciences (NCBS) - National Institutes of Health (NIH) Collaboration - EU-India grid - Department of Atomic Energy Science Research Council (DAE/SRC) - Department of Biotechnology (DBT) | cell, computational, molecule, network, neuronal, neuroscience, simulation, subcellular, systems biology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MUlti SImulation Coordinator has parent organization: SourceForge |
nif-0000-10307 | http://www.nitrc.org/projects/moose | SCR_008031 | SciCrunch Registry | MOOSE | 2026-11-07 11:56:28 | 313 | ||||||||
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EBARDenovo Resource Report Resource Website 1+ mentions |
EBARDenovo (RRID:SCR_011890) | EBARDenovo | software resource | Highly accurate de novo assembly of RNA-Seq with efficient chimera-detection. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01317 | SCR_011890 | SciCrunch Registry | 2026-11-07 11:57:33 | 2 | ||||||||||
|
SeqGene Resource Report Resource Website 1+ mentions |
SeqGene (RRID:SCR_011861) | SeqGene | software resource | An open-source software for mining next-gen sequencing datasets, focusing on post-alignment quality control, SNP and indel identification and annotation, RNA expression quantification, etc. |
is listed by: OMICtools has parent organization: SourceForge |
Open unspecified license | OMICS_01134 | SCR_011861 | SciCrunch Registry | 2026-11-07 11:57:29 | 2 | |||||||||
|
naiveBayesCall Resource Report Resource Website |
naiveBayesCall (RRID:SCR_011866) | naiveBayesCall | software resource | An efficient model-based base-calling algorithm for high-throughput sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01152, biotools:bayescall | https://bio.tools/bayescall | SCR_011866 | SciCrunch Registry | 2026-11-07 11:57:32 | 0 | ||||||||
|
Scalpel Resource Report Resource Website 50+ mentions |
Scalpel (RRID:SCR_012107) | software resource | A software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina). | software package, c++, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25128977 | biotools:scalpel, OMICS_05395 | https://bio.tools/scalpel | SCR_012107 | SciCrunch Registry | 2026-11-07 11:57:27 | 62 | ||||||||
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MToolBox Resource Report Resource Website 50+ mentions |
MToolBox (RRID:SCR_012112) | software resource | Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25028726 | GNU General Public License | OMICS_05466, biotools:mtoolbox | https://bio.tools/mtoolbox | SCR_012112 | SciCrunch Registry | 2026-11-07 11:57:26 | 57 | |||||||
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ReviSTER Resource Report Resource Website |
ReviSTER (RRID:SCR_012113) | software resource | Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23677944 | GNU General Public License | OMICS_05468 | SCR_012113 | SciCrunch Registry | Revise Simple Tandem repeat Error Reads | 2026-11-07 11:57:33 | 0 | |||||||
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SNP ratio test Resource Report Resource Website 1+ mentions |
SNP ratio test (RRID:SCR_012070) | software resource | Software to calculate the number of significant SNPs in pathway divided by the number of SNPs in pathway. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19620097 | GNU General Public License | biotools:snp_ratio_test, OMICS_04390 | https://bio.tools/snp_ratio_test | SCR_012070 | SciCrunch Registry | 2026-11-07 11:57:25 | 2 | |||||||
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VirVarSeq Resource Report Resource Website 10+ mentions |
VirVarSeq (RRID:SCR_012116) | software resource | Software for a low frequency Virus Variant detection pipeline for Illumina data. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25178459 | OMICS_05534 | SCR_012116 | SciCrunch Registry | 2026-11-07 11:57:26 | 13 | |||||||||
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Toxtree Resource Report Resource Website 100+ mentions |
Toxtree (RRID:SCR_012086) | software resource | A full-featured and flexible user-friendly open source software application, which is able to estimate toxic hazard by applying a decision tree approach. | standalone software, web app |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18853299 | OMICS_05024 | SCR_012086 | SciCrunch Registry | 2026-11-07 11:57:25 | 109 | |||||||||
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Viewmol Resource Report Resource Website |
Viewmol (RRID:SCR_012088) | software resource | Software providing a graphical front end for computational chemistry programs. | standalone software, windows, c, python |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
GNU General Public License | OMICS_05057 | https://sources.debian.org/src/viewmol/ | SCR_012088 | SciCrunch Registry | 2026-11-07 11:57:38 | 0 | ||||||||
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Toxmatch Resource Report Resource Website 1+ mentions |
Toxmatch (RRID:SCR_012087) | software resource | A software tool to facilitate chemical similarity calculations. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18617309 | OMICS_05025 | SCR_012087 | SciCrunch Registry | 2026-11-07 11:57:32 | 2 |
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