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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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HIA Resource Report Resource Website |
HIA (RRID:SCR_006865) | HIA | software resource | A sequence alignment tool to align both short and long reads to a reference genome. HIA has two indexes, a hash table index and a suffix array index. The hash table is capable of the direct lookup of a q-gram and the suffix array is very fast in the lookup of a variable length q-gram. Our experiments show that the hybrid of hash table and suffix array is useful at the perspective of speed to map NGS sequencing reads to a reference genome sequence. | matlab, java, command-line |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00666 | SCR_006865 | Hybrid Index based sequence Alignment, HIA - Hybrid Index based sequence Alignment | 2026-08-29 11:22:54 | 0 | ||||||||
|
fitGCP Resource Report Resource Website |
fitGCP (RRID:SCR_006741) | fitGCP | software resource | Software providing a framework for fitting mixtures of probability distributions to genome coverage profiles. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23589648 DOI:10.1093/bioinformatics/btt147 |
BSD License | OMICS_01046 | https://sources.debian.org/src/fitgcp/ | SCR_006741 | fitGCP - Fitting genome coverage distributions with mixture models | 2026-08-29 11:22:49 | 0 | ||||||
|
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 | GASiC - Genome Abundance Similarity Correction, Genome Abundance Similarity Correction | 2026-08-29 11:22:44 | 3 | |||||
|
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 | 2026-08-29 11:22:44 | 0 | ||||||||||
|
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 | QUASR - Cross-platform NGS processing and analysis pipeline in Python | 2026-08-29 11:22:45 | 219 | |||||||
|
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 | Simulate High-Throughput Sequencing Data | 2026-08-29 11:22:43 | 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 | Bioinformatics Named Entity Recognizer for Databases and Software, Bioinformatics Named Entity Recogniser for Databases and Software | 2026-08-29 11:22:44 | 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 | Virtual Microdissection for SNP calling | 2026-08-29 11:22:44 | 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 | 2026-08-29 11:22:51 | 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 | Taxonomic assignment of sequences, TANGO: Taxonomic Assignment in Metagenomics | 2026-08-29 11:22:43 | 246 | ||||||
|
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 | DECONtamination of SEQuence data, decontamination of sequence data | 2026-08-29 11:22:45 | 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 | Monte Carlo eXtreme (MCX) | 2026-08-29 11:22:49 | 2 | ||||||
|
ParticleCall Resource Report Resource Website |
ParticleCall (RRID:SCR_001103) | ParticleCall | software resource | A base-calling algorithm for Illumina DNA sequencing. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22776067 | OMICS_01154 | SCR_001103 | 2026-08-29 11:20:59 | 0 | ||||||||
|
SparseAssembler Resource Report Resource Website 1+ mentions |
SparseAssembler (RRID:SCR_001100) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for memory-efficient genome assembly. It utilizes sparse k-mer. | genome, genomics, genome assembly, k-mer, sequence analysis software, memory |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22537038 | Free, Available for download, Freely available | OMICS_00032 | SCR_001100 | 2026-08-29 11:20:35 | 1 | ||||||||
|
CUDA-EC Resource Report Resource Website 1+ mentions |
CUDA-EC (RRID:SCR_001090) | CUDA-EC | software resource | A fast parallel error correction tool for short reads. | c, gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20426693 | Free, Available for download, Freely available | OMICS_01100, biotools:cuda-ec | https://bio.tools/cuda-ec | SCR_001090 | Compute Unified Device Architecture | 2026-08-29 11:20:43 | 1 | |||||
|
qips Resource Report Resource Website |
qips (RRID:SCR_001092) | qips | software resource | A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase. | command-line, c++, python |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_00457 | SCR_001092 | 2026-08-29 11:20:35 | 0 | ||||||||
|
CrossMap Resource Report Resource Website 10+ mentions |
CrossMap (RRID:SCR_001173) | CrossMap | software resource | A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species. | genome, assembly |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24351709 | GNU General Public License | OMICS_02184 | SCR_001173 | 2026-08-29 11:20:37 | 19 | |||||||
|
Breakway Resource Report Resource Website |
Breakway (RRID:SCR_001180) | Breakway | software resource | A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives. | genome, structural variation, breakpoint |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at Los Angeles; California; USA |
PMID:20126413 | Free, Available for download, Freely available | OMICS_02176 | SCR_001180 | Breakway: Identify Structural Variations in Genomic Data | 2026-08-29 11:20:37 | 0 | ||||||
|
ChIP-seq Resource Report Resource Website 5000+ mentions |
ChIP-seq (RRID:SCR_001237) | ChIP-seq | data analysis software, data processing software, software application, software resource, software toolkit | Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface. | high-throughput sequencing, chromatin immuno precipitation, chip-seq, genome, c |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:27863463 | Free, Available for download, Freely available | OMICS_02103 | https://epd.expasy.org/chipseq/, https://chip-seq.sourceforge.net/ | SCR_001237 | ChIP-seq - Tools for the analysis of ChIP-seq data | 2026-08-29 11:21:00 | 8035 | |||||
|
NGSrich Resource Report Resource Website 10+ mentions |
NGSrich (RRID:SCR_001333) | software resource | Software for target enrichment performance for next-generation sequencing. | standalone software, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22290614 | Free, Available for download, Freely available | OMICS_03603, biotools:ngsrich | https://bio.tools/ngsrich | SCR_001333 | 2026-08-29 11:20:51 | 10 |
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