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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VariationHunter Resource Report Resource Website 10+ mentions |
VariationHunter (RRID:SCR_004865) | VariationHunter | software resource | A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. | structural variation, genome, next-generation sequencing |
is listed by: OMICtools is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:22048523 PMID:20529927 |
OMICS_00328 | SCR_004865 | VariationHunter-CommonLaw | 2026-09-12 12:56:17 | 12 | |||||||
|
Pythia Resource Report Resource Website 50+ mentions |
Pythia (RRID:SCR_004952) | software resource | Pythia is an open source thermodynamically oriented primer design python module. Pythia can be used in two ways. 1. Executable binaries only: under windows with cygwin and python 2.5 (built with mingw, that comes with the cygwin release). These executables allow the user to index DNA files for primer specificity search, design one primer pair per region, and tile regions with PCR amplicons. 2. A python module: under windows with cygwin, python2.5, numpy, swig, and mingw, or under linux with python2.4 or later, numpy, and swig (everything but numpy should be pre-installed on a normal linux system). The module gets you everything that the binaries get you, in a more pythonic framework. This package also includes modules for computing DNA binding and folding energies using the partition function approach with publicly available thermodynamic data. Usage documentation is in the downloads. | has parent organization: SourceForge | PMID:19528077 | nlx_91969 | SCR_004952 | 2026-09-12 12:56:19 | 50 | ||||||||||
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cortex var Resource Report Resource Website 1+ mentions |
cortex var (RRID:SCR_005081) | cortex_var | software resource | A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal). cortex_var features * Variant discovery by de novo assembly - no reference genome required * Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them. * Capable of calling SNPs, indels, inversions, complex variants, small haplotypes * Extremely accurate variant calling - see our paper for base-pair-resolution validation of entire alleles (rather than just breakpoints) of SNPs, indels and complex variants by comparison with fully sequenced (and finished) fosmids - a level of validation beyond that demanded of any other variant caller we are aware of - currently cortex_var is the most accurate variant caller for indels and complex variants. * Capable of aligning a reference genome to a graph and using that to call variants * Support for comparing cases/controls or phenotyped strains * Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM | genome assembly, variation analysis, sequence, variation, genotype variant, haploid, diploid, snp, indel, inversion, variant, haplotype, de novo assembly, genotyping, variant-calling, population analysis, population assembly |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:22231483 | GNU General Public License, v3, Acknowledgement requested | OMICS_00056 | SCR_005081 | cortex_var - for variant and population assembly | 2026-09-12 12:56:20 | 3 | ||||||
|
Bambus Resource Report Resource Website |
Bambus (RRID:SCR_005068) | Bambus | software resource | Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny. | scaffolding |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21926123 | Open unspecified license | OMICS_01432 | http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus | SCR_005068 | Bambus 2, Bambus 2.0 | 2026-09-12 12:56:20 | 0 | |||||
|
G-BLASTN Resource Report Resource Website |
G-BLASTN (RRID:SCR_005062) | G-BLASTN | software resource | A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. | parallel computation 4, blast, alignment, nucleotide, gpu, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BLAST has parent organization: Hong Kong Baptist University; Hong Kong; China has parent organization: SourceForge |
Hong Kong Baptist University; Hong Kong; China FRG2/11-12/158; NVIDIA |
PMID:24463183 | Free | OMICS_02263, biotools:g-blastn | http://sourceforge.net/projects/gblastn/, https://bio.tools/g-blastn | SCR_005062 | 2026-09-12 12:56:20 | 0 | |||||
|
VFS Resource Report Resource Website 1+ mentions |
VFS (RRID:SCR_005138) | VFS | software resource | A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. | ubuntu, debian, high-throughput sequencing, virus, reconstruct, fusion transcript, transcript, integration, fusion, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23314323 | GNU General Public License, v3 | OMICS_00224, biotools:viralfusionseq | https://bio.tools/viralfusionseq | SCR_005138 | ViralFusionSeq, ViralFusionSeq (VFS) | 2026-09-12 12:56:21 | 1 | |||||
|
COVA Resource Report Resource Website 50+ mentions |
COVA (RRID:SCR_005175) | COVA | software resource | A variant annotation and comparison tool for next-generation sequencing. It annotates the effects of variants on genes and compares those among multiple samples, which helps to pinpoint causal variation(s) relating to phenotype. | next-generation sequencing, variant annotation, variant, annotation, gene, genetic variation, phenotype |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00171 | SCR_005175 | COVA - Comparison of variants and functional annotation, Comparison of variants and functional annotation | 2026-09-12 12:56:22 | 60 | ||||||||
|
QuRe Resource Report Resource Website 1+ mentions |
QuRe (RRID:SCR_005209) | QuRe | software resource | A software program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) next-generation sequencing (NGS) data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions. | next-generation sequencing, virus, long read, reconstruction |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00230 | SCR_005209 | qure - software for viral quasispecies reconstruction from next-gen seq. data | 2026-09-12 12:56:22 | 6 | ||||||||
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UnoSeq Resource Report Resource Website 1+ mentions |
UnoSeq (RRID:SCR_005116) | UnoSeq | software library, software resource, software toolkit | A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists. | java, expression profile, next generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20194116 | OMICS_01296 | SCR_005116 | UnoSeq - Expression profiling with next generation sequencing without a reference genome | 2026-09-12 12:56:21 | 1 | |||||||
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ORMAN Resource Report Resource Website 1+ mentions |
ORMAN (RRID:SCR_005188) | ORMAN | software resource | A software tool for resolving multi-mappings within an RNA-Seq SAM file. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24130305 | OMICS_01284, biotools:orman | https://bio.tools/orman | SCR_005188 | ORMAN : Optimal Resolution of Ambiguous RNA-Seq Multi-mappings in the Presence of Novel Isoforms | 2026-09-12 12:56:22 | 4 | ||||||
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SeqAnt Resource Report Resource Website 1+ mentions |
SeqAnt (RRID:SCR_005186) | SeqAnt | analysis service resource, data analysis service, production service resource, service resource, software resource | A free web service and open source software package that performs rapid, automated annotation of DNA sequence variants (single base mutations, insertions, deletions) discovered with any sequencing platform. Variant sites are characterized with respect to their functional type (Silent, Replacement, 5' UTR, 3' UTR, Intronic, Intergenic), whether they have been previously submitted to dbSNP, and their evolutionary conservation. Annotated variants can be viewed directly on the web browser, downloaded in a tab delimited text file, or directly uploaded in a Browser Extended Data (BED) format to the UCSC genome browser. SeqAnt further identifies all loci harboring two or more coding sequence variants that help investigators identify potential compound heterozygous loci within exome sequencing experiments. In total, SeqAnt resolves a significant bottleneck by allowing an investigator to rapidly prioritize the functional analysis of those variants of interest. | annotation, dna sequence variant, single base mutation, insertion, deletion, sequencing, mutation, variant, sequence variant, perl, sequence, genome |
is listed by: OMICtools has parent organization: Emory University; Georgia; USA has parent organization: SourceForge |
PMID:20854673 | GNU General Public License, v2 | OMICS_00182 | SCR_005186 | SeqAnt - Sequence Annotator | 2026-09-12 12:56:22 | 2 | ||||||
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Ergatis Resource Report Resource Website 1+ mentions |
Ergatis (RRID:SCR_005377) | Ergatis | software resource | A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level. | workflow, bioinformatics, workflow management, pipeline, computation, genomics, genome, processing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Maryland School of Medicine; Maryland; USA |
PMID:20413634 | Artistic License | OMICS_01140 | SCR_005377 | ergatis: workflow creation and monitoring interface | 2026-09-12 12:56:25 | 2 | ||||||
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PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | data or information resource, data repository, database, service resource, software resource, storage service resource | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | 2026-09-12 12:56:25 | 32 | ||||||
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MolBioLib Resource Report Resource Website |
MolBioLib (RRID:SCR_005372) | MolBioLib | software resource | A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++. | c++, next-generation sequencing, genomic, analysis, genome |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815363 | OMICS_01145 | SCR_005372 | MolBioLib: C++11 framework for rapid develop and deploy of bioinformatic tasks | 2026-09-12 12:56:25 | 0 | |||||||
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SPLITREAD Resource Report Resource Website 1+ mentions |
SPLITREAD (RRID:SCR_005264) | SPLITREAD | software resource | Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data. | deletion, insertion, indel, genome, exome |
is listed by: OMICtools is related to: drFAST is related to: mrFAST is related to: mrsFAST is related to: VariationHunter is related to: NovelSeq is related to: mrCaNaVaR has parent organization: SourceForge |
OMICS_00323 | SCR_005264 | SPLITREAD - Split read based INDEL/SV Caller | 2026-09-12 12:56:23 | 3 | ||||||||
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Maq Resource Report Resource Website 50+ mentions |
Maq (RRID:SCR_005485) | Maq | software resource | A set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way. | command-line, curses/ncurses, opengl, c, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
DOI:10.1101/gr.078212.108 | GNU General Public License, v2 | OMICS_00668, biotools:maq | https://bio.tools/maq, https://sources.debian.org/src/maq/ | SCR_005485 | mapass2, Mapping and Assembly with Quality, Mapping and Assembly with Qualities, Maq: Mapping and Assembly with Qualities | 2026-09-12 12:56:26 | 74 | |||||
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MACE Resource Report Resource Website 1000+ mentions |
MACE (RRID:SCR_005520) | MACE | software resource | A bioinformatics tool dedicated to analyze ChIP-exo data: 1) Sequencing depth normalization and nucleotide composition bias correction. 2) Signal consolidation and noise reduction. 3) Single base resolution border detection. 4) Border matching. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00520 | SCR_005520 | MACE: Model based Analysis of ChIP-exo | 2026-09-12 12:56:27 | 1192 | |||||||||
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TreQ Resource Report Resource Website |
TreQ (RRID:SCR_005505) | TreQ | software resource | A software read mapper for high-throughput DNA sequencing reads, in particular one to several hundred nucleotides in length, and for large edit distance between sequencing read and match in the reference genome. It can cope particularly well with indels for single-best hit recall of 200nt reads simulated from the human reference genome. TreQ performs best at a running time comparable to BWA at large edit distance settings. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Rutgers University; New Jersey; USA |
PMID:22962448 | GNU General Public License | OMICS_00695, biotools:treq | https://bio.tools/treq | SCR_005505 | TreQ: Indel-tolerant Read Mapper | 2026-09-12 12:56:27 | 0 | |||||
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netClass Resource Report Resource Website |
netClass (RRID:SCR_005672) | netClass | software resource | An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM). | protein-protein interaction network, biomarker discovery, classification, micoarray, gene expression profile, protein-protein interaction, gene expression, gene, biomarker |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24443376 | Free, Public | OMICS_02241 | SCR_005672 | 2026-09-12 12:56:29 | 0 | |||||||
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go-moose Resource Report Resource Website |
go-moose (RRID:SCR_005666) | go-moose | data analysis software, data processing software, software application, software resource | go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, slimmer-type tool, analysis, gene ontology, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: go-perl is related to: go-db-perl has parent organization: SourceForge has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: Lawrence Berkeley National Laboratory |
Free for academic use | nlx_149189 | SCR_005666 | 2026-09-12 12:56:29 | 0 |
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