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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GESND Resource Report Resource Website |
GESND (RRID:SCR_005179) | GESND | software resource | A software package and a pipeline for identifying causal mutations for rare congenital diseases by next-generation sequencing. Features * one-stop solution for identifying causal mutations of rare genetic diseases * detect wide-spctrum variants, including medium and large sized indels, and tandem repeats * annotate and filter variants * prioritize candidate variants | next-generation sequencing, mutation, variant, indel, tandem repeat |
is listed by: OMICtools has parent organization: SourceForge |
Rare congenital disease | OMICS_00175 | SCR_005179 | Genetic Screening and Diagnosis, GESND - Genetic Screening and Diagnosis | 2026-08-01 12:02:47 | 0 | |||||||
|
AnnTools Resource Report Resource Website 1+ mentions |
AnnTools (RRID:SCR_005170) | AnnTools | software resource | Software tool for annotating single nucleotide substitutions (SNP/SNV), small insertions/deletions (indels), and copy number variations (CNV) calls generated from sequencing and microarray data. Only human genome build 37/hg19 can be annotated at this time. | single nucleotide substitution, snp, snv, indel, copy number variation, sequencing, microarray, linux, unix, mac osx, python, mysql, genome annotation, genome, annotation |
is listed by: OMICtools has parent organization: SourceForge |
BSD License | OMICS_00166 | SCR_005170 | 2026-08-01 12:02:50 | 4 | ||||||||
|
HIVCD Resource Report Resource Website |
HIVCD (RRID:SCR_005201) | HIVCD | software resource | Informatics software tool to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage. | java, perl, contamination, sequencing, error, pairwise comparison, testing, analysis, contamination screening |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23583427 | Apache License, v2 | OMICS_00220 | SCR_005201 | HIVCD - Informatics tool for contamination screening in the HIV sequencing lab, HIV Contamination Detection | 2026-08-01 12:02:50 | 0 | ||||||
|
ASOoViR Resource Report Resource Website |
ASOoViR (RRID:SCR_005161) | ASOoViR | software resource | A set of Ruby modules to annotate consequence terms, defined by the Sequence Ontology, of variants (SNP/SNVs, INDELs, SVs, CNAs) using Ensembl gene sets. Prior to annotation of variants an Ensembl gene set and reference coding sequences are loaded into memory from a database file, which can be downloaded or generated by the user from reference files. This allows rapid annotation of variants, making it suitable for annotation of whole genome scale calls. Annotation is performed on a transcript level basis, identifying associated sequence ontology terms for affected and nearby transcripts. Default output can be obtained on a gene basis, summarising the consequences for each gene affected, or on a transcript level basis. Output information is also readily customisable using user-generated scripts. | ruby, annotate |
is listed by: OMICtools is related to: SO has parent organization: SourceForge |
OMICS_00167 | SCR_005161 | Annotating Sequence Ontology of Variants in Ruby, ASOoViR - Annotating Sequence Ontology of Variants in Ruby | 2026-08-01 12:02:56 | 0 | ||||||||
|
SnpEff Resource Report Resource Website 5000+ mentions |
SnpEff (RRID:SCR_005191) | SnpEff | software resource | Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs. | genome, genetic variant, annotation, effect, variant, gene, cancer variant, gatk, hgsv, single nucleotide polymorphisms, genome sequence, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: GATK has parent organization: SourceForge has parent organization: Wayne State University; Michigan; USA works with: SnpSift |
Cancer | PMID:22728672 | Free, Freely available | biotools:snpeff, OMICS_00186 | https://bio.tools/snpeff, https://sources.debian.org/src/snpeff/ | SCR_005191 | SnpEff - Genetic variant annotation and effect prediction toolbox | 2026-08-01 12:02:57 | 5186 | ||||
|
inGAP Resource Report Resource Website 10+ mentions |
inGAP (RRID:SCR_005261) | inGAP | software resource | Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations. | structural variation, genome, next-generation sequence, genome analysis, alignment, single nucleotide polymorphism, insertion, deletion, indel, inversion, translocation, windows, linux, macos/x, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Fudan University; Shanghai; China has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_00319, biotools:ingap | https://bio.tools/ingap | SCR_005261 | inGAP-sv, inGAP-sv: structural variation detection and visualization, integrative next-generation genome analysis pipeline | 2026-08-01 12:02:49 | 29 | |||||||
|
CoverageCalculator Resource Report Resource Website 1+ mentions |
CoverageCalculator (RRID:SCR_005352) | CoverageCalculator | software resource | Small and very fast utility to calculate X-coverage from Next-Generation-Sequencing data. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01164 | SCR_005352 | 2026-08-01 12:02:52 | 2 | |||||||||
|
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 | mrFAST - Micro Read Fast Alignment Search Tool, Micro Read Fast Alignment Search Tool | 2026-08-01 12:02:54 | 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 | 2026-08-01 12:02:59 | 0 | ||||||||
|
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 | CUSHAW2, CUSHAW3 | 2026-08-01 12:02:54 | 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 | 2026-08-01 12:02:57 | 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 | Text Alignment Viewer | 2026-08-01 12:03:00 | 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 | 2026-08-01 12:02:56 | 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 | Cancergrid Image Scorer | 2026-08-01 12:02:55 | 0 | ||||||||
|
dna-bison Resource Report Resource Website 1+ mentions |
dna-bison (RRID:SCR_005913) | dna-bison | software resource | Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00582 | SCR_005913 | 2026-08-01 12:03:03 | 1 | ||||||||||
|
PowerMap Resource Report Resource Website 1+ mentions |
PowerMap (RRID:SCR_006721) | PowerMap | software resource | Software tool specifically designed for neuroimaging data that implements theoretical power calculation algorithms based on non-central random field theory. It can also calculate power for statistical analyses with FDR (false discovery rate) corrections. This GUI (graphical user interface)-based tool enables neuroimaging researchers without advanced knowledge in imaging statistics to calculate power and sample size in the form of 3D images. This tool is currently under limited release for beta testing. At this time, only users that have been directed to this site by the PowerMap developers will receive support. | neuroimaging, statistical analyses, false discovery rate, 3d spatial image, power calculation, sample size |
has parent organization: Wake Forest School of Medicine; North Carolina; USA has parent organization: SourceForge |
NINDS NS059793 | PMID:22644868 | Free, Public | nlx_152808 | SCR_006721 | 2026-08-01 12:03:12 | 3 | ||||||
|
Samscope Resource Report Resource Website |
Samscope (RRID:SCR_006715) | Samscope | software resource | A lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments. | c++, visualization, opengl, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
GNU Affero General Public License | OMICS_00892 | SCR_006715 | samscope - A lightweight OpenGL SAM/BAM viewer | 2026-08-01 12:03:12 | 0 | |||||||
|
DMEAS Resource Report Resource Website 1+ mentions |
DMEAS (RRID:SCR_006679) | DMEAS | software resource | A user-friendly DNA methylation analysis tool for DNA methylation pattern extraction, DNA methylation level estimation, DNA methylation entropy analysis and multi-sample comparison. It was developed in order to assess the DNA methylation variations for a given genomic locus or genome-wide methylation data. | c# |
is listed by: OMICtools has parent organization: SourceForge |
Creative Commons Attribution License | OMICS_00598 | SCR_006679 | DNA Methylation Entropy Analysis Software, DMEAS - DNA Methylation Entropy Analysis Software | 2026-08-01 12:03:14 | 1 | |||||||
|
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 | 2026-08-01 12:03:14 | 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 | 2026-08-01 12:03:12 | 0 |
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