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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-07-25 12:06:27 | 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 | 2026-07-25 12:06:28 | 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 | 2026-07-25 12:06:31 | 246 | ||||||
|
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 | 2026-07-25 12:06:06 | 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 | 2026-07-25 12:06:07 | 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 | 2026-07-25 12:06:10 | 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 | 2026-07-25 12:06:09 | 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 | 2026-07-25 12:06:11 | 1 | ||||||||||
|
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 | 2026-07-25 12:05:47 | 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 | 2026-07-25 12:05:50 | 0 | |||||||
|
PASHA Resource Report Resource Website 10+ mentions |
PASHA (RRID:SCR_004455) | PASHA | software resource | A parallel short read assembler for large genomes using de Bruijn graphs. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21867511 | OMICS_00024 | SCR_004455 | 2026-07-25 12:05:53 | 10 | |||||||||
|
SnoopCGH Resource Report Resource Website 1+ mentions |
SnoopCGH (RRID:SCR_004420) | SnoopCGH | software resource | A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:19687029 | biotools:snoopcgh, OMICS_00736 | https://bio.tools/snoopcgh | SCR_004420 | 2026-07-25 12:05:50 | 2 | |||||||
|
LMAT Resource Report Resource Website 10+ mentions |
LMAT (RRID:SCR_004646) | LMAT | software resource | Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads. | c++, metagenomic, metagenomic classification, genome, virus, taxonomy, database, reference genome |
is listed by: OMICtools has parent organization: Lawrence Livermore National Laboratory has parent organization: SourceForge |
PMID:23828782 | Open unspecified license | OMICS_02285 | SCR_004646 | Livermore Metagenomics Analysis Toolkit | 2026-07-25 12:05:52 | 15 | ||||||
|
USeq Resource Report Resource Website 100+ mentions |
USeq (RRID:SCR_004753) | USeq | software resource | A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00499, biotools:useq | https://bio.tools/useq | SCR_004753 | 2026-07-25 12:05:54 | 124 | ||||||||
|
SVMerge Resource Report Resource Website 10+ mentions |
SVMerge (RRID:SCR_004777) | SVMerge | software resource | Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available. | structural variant, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21194472 | biotools:svmerge, OMICS_00325 | https://bio.tools/svmerge | SCR_004777 | SVMerge - Enhanced structural variant and breakpoint detection | 2026-07-25 12:05:57 | 19 | ||||||
|
T-lex Resource Report Resource Website 1+ mentions |
T-lex (RRID:SCR_005134) | T-lex | software resource | Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data. | transposable element, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California has parent organization: SourceForge |
GNU General Public License | biotools:t-lex2, OMICS_00121 | https://bio.tools/t-lex2 | SCR_005134 | T-lex package | 2026-07-25 12:06:02 | 4 | ||||||
|
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 | 2026-07-25 12:06:02 | 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 | 2026-07-25 12:05:59 | 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 | 2026-07-25 12:06:00 | 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 | 2026-07-25 12:06:00 | 0 |
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