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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SourceForge Resource Report Resource Website 500+ mentions |
SourceForge (RRID:SCR_004365) | data access protocol, software resource, web service | Web based service that offers software developers centralized online location to control and manage free and open source software projects. Open source software tool and business public software platform. | software, platform, tool, resource, catalog, community, project, , FASEB list |
lists: Clinical Measurement Ontology lists: Measurement Method Ontology lists: CHEBI lists: Fly Taxonomy lists: Software Ontology lists: MIAPA lists: Comparative Data Analysis Ontology lists: SOAPfuse lists: MetAssign lists: Avalon Cheminformatics Toolkit lists: FMAToolbox lists: Multivariate Analysis of Transcript Splicing is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox is related to: BVA import/export EEGLAB plugin is parent organization of: SP-Designer is parent organization of: BlackOPs is parent organization of: UTR is parent organization of: CG-Pipeline is parent organization of: iMethy is parent organization of: dprimer is parent organization of: Dissect is parent organization of: AbMining ToolBox is parent organization of: siRNArules is parent organization of: MysiRNA-designer is parent organization of: D-Tailor is parent organization of: BioLemmatizer is parent organization of: exomeSuite is parent organization of: Sequence Read Format is parent organization of: BLASTPLOT is parent organization of: Magnolya is parent organization of: GMATo is parent organization of: GemSIM is parent organization of: Grinder is parent organization of: MS-Spectre is parent organization of: Quant is parent organization of: GProX is parent organization of: PeptideProphet is parent organization of: ProteinProphet is parent organization of: OMSSAPercolator is parent organization of: Flicker is parent organization of: LIPAGE is parent organization of: fqzcomp is parent organization of: ArrayPlex is parent organization of: cuteNMR is parent organization of: Jnomics is parent organization of: JMolDraw is parent organization of: CGAP-Align is parent organization of: Kinannote is parent organization of: ParseCNV is parent organization of: riboPicker is parent organization of: GENSENG is parent organization of: AS-Peak is parent organization of: FunctSNP is parent organization of: Micro-Analyzer is parent organization of: Reprever is parent organization of: POPBAM is parent organization of: pyQPCR is parent organization of: miRprimer is parent organization of: BAIT is parent organization of: fourSig is parent organization of: MaryGold is parent organization of: TOPPAS is parent organization of: Ishtar is parent organization of: mzMatch is parent organization of: ViReMa is parent organization of: VariantMaster is parent organization of: NGS-Cleaner is parent organization of: drFAST is parent organization of: PhenoFam is parent organization of: GMcloser is parent organization of: Bycom is parent organization of: NGS tools for the novice is parent organization of: Opera is parent organization of: SRMA is parent organization of: DeNovoGear is parent organization of: TriageTools is parent organization of: detecttd is parent organization of: FastUniq is parent organization of: FineSplice is parent organization of: AutoAssemblyD is parent organization of: CUDA-EC is parent organization of: qips is parent organization of: SparseAssembler is parent organization of: ParticleCall is parent organization of: skewer is parent organization of: CrossMap is parent organization of: Breakway is parent organization of: MUMmerGPU is parent organization of: PHACCS is parent organization of: ChIP-seq is parent organization of: Mutascope is parent organization of: metabnorm is parent organization of: KAnalyze is parent organization of: NGSrich is parent organization of: Mugsy is parent organization of: BACContigEditor is parent organization of: HAPLOPAINTER is parent organization of: PennSeq is parent organization of: DNACLUST is parent organization of: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets is parent organization of: Ray is parent organization of: openADAM is parent organization of: DMET-Analyzer is parent organization of: SNVer is parent organization of: Cake is parent organization of: Matchprot is parent organization of: NIDB - Neuroinformatics Database is parent organization of: RUbioSeq is parent organization of: SCRalyze is parent organization of: TARQUIN is parent organization of: Rainbow is parent organization of: GLProbs is parent organization of: ANDES is parent organization of: Batch Oligo Selection Script is parent organization of: rDock is parent organization of: Biologic Stylus is parent organization of: MIPE is parent organization of: FAS-DPD is parent organization of: mrsFAST is parent organization of: mrCaNaVaR is parent organization of: SaskPrimerFS is parent organization of: XORRO is parent organization of: SALT is parent organization of: Gemi is parent organization of: Vertebrate Trait Ontology is parent organization of: Xournal is parent organization of: Metabolomics Standards Initiative is parent organization of: SpliCQ is parent organization of: ORFprimer is parent organization of: JCVI Primer Designer is parent organization of: deFuse is parent organization of: Amplicon is parent organization of: PrimerSeq is parent organization of: Niftilib is parent organization of: GEOSS is parent organization of: GEPAT is parent organization of: Jmol is parent organization of: SeqExpress is parent organization of: InsertionMapper is parent organization of: HLASeq is parent organization of: BamView is parent organization of: CB-Commander is parent organization of: Vanator is parent organization of: SnoopCGH is parent organization of: PASHA is parent organization of: USeq is parent organization of: SVMerge is parent organization of: Pythia is parent organization of: Bambus is parent organization of: cortex var is parent organization of: UnoSeq is parent organization of: VFS is parent organization of: ASOoViR is parent organization of: AnnTools is parent organization of: COVA is parent organization of: GESND is parent organization of: ORMAN is parent organization of: SnpEff is parent organization of: HIVCD is parent organization of: QuRe is parent organization of: inGAP is parent organization of: SPLITREAD is parent organization of: (at)Note is parent organization of: CoverageCalculator is parent organization of: MolBioLib is parent organization of: Ergatis is parent organization of: SolexaQA is parent organization of: CUSHAW2-GPU is parent organization of: Maq is parent organization of: mrFAST is parent organization of: TreQ is parent organization of: Hadoop-BAM is parent organization of: MACE is parent organization of: Sybil is parent organization of: cancergrid-tma is parent organization of: SAMtools Text Alignment Viewer is parent organization of: Staden Package is parent organization of: Maqview is parent organization of: NGSView is parent organization of: go-moose is parent organization of: netClass is parent organization of: ESTScan is parent organization of: MAGMA is parent organization of: ALCHEMY is parent organization of: Brain Networks is parent organization of: Neurofitter is parent organization of: dna-bison is parent organization of: BLESS is parent organization of: Object-Oriented Development Interface for NMR is parent organization of: HTQC is parent organization of: OBO Tracker: Plant Ontology (PO) TERM requests is parent organization of: COHCAP is parent organization of: Picard is parent organization of: SpliceGrapher is parent organization of: Blox is parent organization of: DMEAS is parent organization of: Samscope is parent organization of: GARM is parent organization of: fitGCP is parent organization of: POLGUI - Matlab Polhemus Interface is parent organization of: Next-gen Sequencing Scaffolding Tool is parent organization of: GASiC is parent organization of: Qudaich is parent organization of: Virmid is parent organization of: BIGpre is parent organization of: bioNerDS is parent organization of: mubiomics is parent organization of: GBS barcode splitter is parent organization of: Adverse Event Ontology is parent organization of: TaxoAssignement is parent organization of: QUASR is parent organization of: simhtsd is parent organization of: BMDExpress is parent organization of: HIA is parent organization of: Mesh-based Monte Carlo (MMC) is parent organization of: MIGen is parent organization of: BAMStats is parent organization of: Monte Carlo eXtreme is parent organization of: DeconSeq is parent organization of: neurospy is parent organization of: Taipan is parent organization of: BRIG is parent organization of: GenoTan is parent organization of: Multiscale Object Orientation Simulation Environment is parent organization of: BioMail is parent organization of: SeqPig is parent organization of: CUDASW++ is parent organization of: OrChem is parent organization of: Gecko is parent organization of: LIBEEP is parent organization of: MarsBaR region of interest toolbox for SPM is parent organization of: SCALCE is parent organization of: CLIIQ is parent organization of: vipR is parent organization of: MIRA is parent organization of: Celera assembler is parent organization of: SVDetect is parent organization of: CONTRA is parent organization of: FindPeaks is parent organization of: PeakRanger is parent organization of: Arpeggio is parent organization of: BWA is parent organization of: CloudBurst is parent organization of: ERNE is parent organization of: PPSEQ is parent organization of: SEAL is parent organization of: Genovar is parent organization of: XDrawChem is parent organization of: DNPTrapper is parent organization of: Hawkeye is parent organization of: TagCleaner is parent organization of: ECHO is parent organization of: SeqGene is parent organization of: naiveBayesCall is parent organization of: EBARDenovo is parent organization of: Ray Meta is parent organization of: Scramble is parent organization of: PerlPrimer is parent organization of: CowCoDA is parent organization of: MZmine is parent organization of: OBI-Warp is parent organization of: OpenMS is parent organization of: CPFP is parent organization of: TOPP is parent organization of: swissPIT is parent organization of: Antilope is parent organization of: ICPL ESIQuant is parent organization of: MFPaQ is parent organization of: ProteoWizard is parent organization of: Maltcms is parent organization of: multiplierz is parent organization of: ADTEx is parent organization of: MatNMR is parent organization of: GSim is parent organization of: RASP is parent organization of: TE-locate is parent organization of: FIGG is parent organization of: DIYA is parent organization of: MrBayes is parent organization of: Fastphylo is parent organization of: PhyloTreePruner is parent organization of: SNP ratio test is parent organization of: FingerID is parent organization of: proTRAC is parent organization of: HopeMap is parent organization of: SketchEl is parent organization of: GLARE is parent organization of: MCDL is parent organization of: NetMODE is parent organization of: Toxtree is parent organization of: Toxmatch is parent organization of: Viewmol is parent organization of: QuteMol is parent organization of: PBJelly is parent organization of: SAM format is parent organization of: COBRApy is parent organization of: ORCA is parent organization of: Bionotate is parent organization of: Knowtator is parent organization of: MMAX2 is parent organization of: LAITOR is parent organization of: Connecting Overlapped Pair-End reads is parent organization of: iPapers is parent organization of: PyPedal is parent organization of: miRPlant is parent organization of: Simulate PCR is parent organization of: Scalpel is parent organization of: SAT-Assembler is parent organization of: diCal-IBD is parent organization of: MToolBox is parent organization of: ReviSTER is parent organization of: Ionwinze is parent organization of: VirVarSeq is parent organization of: GeneVenn is parent organization of: Pegasus-fus is parent organization of: GenoSIGHT is parent organization of: ISDTool is parent organization of: cnvCapSeq is parent organization of: EC2KEGG is parent organization of: eALPS is parent organization of: LDx is parent organization of: PLEK is parent organization of: NAIL is parent organization of: iMSAT is parent organization of: PrimerProspector is parent organization of: NESmapper is parent organization of: DHAC is parent organization of: Musite is parent organization of: PhosphoSiteAnalyzer is parent organization of: xMSanalyzer is parent organization of: A5-miseq is parent organization of: CNV Workshop is parent organization of: EXCAVATOR-tool is parent organization of: Krona is parent organization of: Trowel is parent organization of: Acacia is parent organization of: miRDeep* is parent organization of: CloudAligner is parent organization of: ProbeSelect is parent organization of: SeqGenome Browser is parent organization of: KungFq is parent organization of: SAMZIP is parent organization of: EDNA is parent organization of: MSAProbs is parent organization of: Onco-STS is parent organization of: ChIPOTle Peak Finder is parent organization of: NxGview is parent organization of: BSmapper is parent organization of: Flexbar is parent organization of: QcReads is parent organization of: HECTOR is parent organization of: SHREC is parent organization of: hiCtools is parent organization of: Swift is parent organization of: TraceTuner is parent organization of: seqMINER is parent organization of: MIREAP is parent organization of: miRDeep-P is parent organization of: ncPRO-seq is parent organization of: vcf2MSAT is parent organization of: SAMMate is parent organization of: FishingCNV is parent organization of: NGSpeAnalysis is parent organization of: Bamformatics is parent organization of: IBDLD is parent organization of: HATS is parent organization of: SolSNP is parent organization of: Trinity is parent organization of: SNPTools is parent organization of: MendelScan is parent organization of: LoFreq is parent organization of: GENE-counter is parent organization of: RNA CoMPASS is parent organization of: VCAKE is parent organization of: LOCAS is parent organization of: Contrail is parent organization of: AMOS is parent organization of: VDJFasta is parent organization of: RDP FrameBot is parent organization of: Celera Genome Browser is parent organization of: AutoMap is parent organization of: DSP is parent organization of: Neuroimaging in Python is parent organization of: cnvHiTSeq is parent organization of: Easyfig is parent organization of: bisReadMapper is parent organization of: palfinder is parent organization of: sam comp is parent organization of: CongrPE is parent organization of: CallSim is parent organization of: Tuxedo is parent organization of: SAPAS is parent organization of: iso2mesh is parent organization of: Telescoper is parent organization of: HeurAA is parent organization of: CoNIFER is parent organization of: DynamicProg is parent organization of: SOCS is parent organization of: BEADS is parent organization of: miRSeqNovel is parent organization of: PIA is parent organization of: ChimeraSlayer is parent organization of: RDXplorer is parent organization of: SeqTRACS is parent organization of: Crossbow is parent organization of: Hanalyzer is parent organization of: QUAST is parent organization of: Drosophila anatomy and development ontologies is parent organization of: Diffusion Tensor Imaging ToolKit is parent organization of: OLORIN is parent organization of: NovelSeq is parent organization of: SobekCM is parent organization of: NEMO Ontology is parent organization of: Mindtouch DekiWiki is parent organization of: MGED Ontology is parent organization of: SPInDel is parent organization of: LMAT is parent organization of: VariationHunter is parent organization of: G-BLASTN is parent organization of: T-lex is parent organization of: SeqAnt is parent organization of: PAZAR is parent organization of: CUSHAW is parent organization of: TMAJ is parent organization of: Manatee is parent organization of: HOLLOW is parent organization of: OWL API is parent organization of: Bioelectromagnetism Matlab Toolbox is parent organization of: Predictive Networks is parent organization of: Centroid Trajectory Analysis is parent organization of: PowerMap is parent organization of: BarraCUDA is parent organization of: FastSemSim is parent organization of: Wisconsin White Matter Hyperintensities Segmentation Toolbox is parent organization of: ArrayOligoSelector hosts: Batman-Seq |
nlx_38463 | SCR_004365 | 2026-08-29 11:27:43 | 923 | ||||||||||
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Wisconsin White Matter Hyperintensities Segmentation Toolbox Resource Report Resource Website 1+ mentions |
Wisconsin White Matter Hyperintensities Segmentation Toolbox (RRID:SCR_009652) | W2MHS | data processing software, image analysis software, segmentation software, software application, software library, software resource, software toolkit | An open source MATLAB toolbox designed for detecting and quantifying White Matter Hyperintensities(WMH) in Alzheimer?s and aging related neurological disorders.Our toolbox provides a self-sufficient set of tools for segmenting these WMHs reliably and further quantifying their burden for down-processing studies. WMHs arise as bright regions on T2-weighted FLAIR images. They reflect comorbid neural injury or cerebral vascular disease burden. Their precise detection is of interest in Alzheimer?s disease (AD) with regard to its prognosis. | computational neuroscience, matlab, nifti, white matter hyperintensity, c++, matlab, ms windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM is related to: SourceForge has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Alzheimer's disease, Aging, Neurological disorder | Academic Free License | nlx_156021 | SCR_009652 | WM Hyperintensities Segmentation Toolbox | 2026-08-29 11:23:38 | 2 | ||||||
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BVA import/export EEGLAB plugin Resource Report Resource Website 1+ mentions |
BVA import/export EEGLAB plugin (RRID:SCR_016333) | bva-io | software application, software resource, software toolkit | Software package for interfacing the Brain Vision Analyser data files (load/save) for ongoing development of Matlab routines . This package is also compatible with the EEGLAB software, and may be uncompressed in the plugin folder of this software. | interfacing, brain, vision, analyser, data, file, load, save, Matlab, routine, compatible, EEGLAB |
is related to: SourceForge is related to: EEGLAB is related to: MATLAB |
Free, Available for download, Freely available | SCR_016333 | Brain Vision Analyser | 2026-08-29 11:31:20 | 4 | ||||||||
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NIDB - Neuroinformatics Database Resource Report Resource Website 1+ mentions |
NIDB - Neuroinformatics Database (RRID:SCR_002488) | NIDB | data management software, data or information resource, database, software application, software resource | Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data. | connectome file format, clinical neuroinformatics, computational neuroscience, computed tomography, imaging genomics, interfile, javascript, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
PMID:25888923 | Free, Available for download, Freely available | nlx_155882 | http://www.nitrc.org/projects/nidb | http://nidb.sourceforge.net/ | SCR_002488 | Neuroinformatics Database | 2026-08-29 11:21:06 | 2 | ||||
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SCRalyze Resource Report Resource Website 10+ mentions |
SCRalyze (RRID:SCR_002542) | SCRalyze | data analysis software, data processing software, software application, software resource | A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models. | eeg, meg, electrocorticography, matlab, modeling, os independent, quantification, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
Free, Available for download, Freely available | nlx_155950 | http://www.nitrc.org/projects/scralyze | SCR_002542 | SCRalyze - A matlab environment for model-based psychophysiology | 2026-08-29 11:21:16 | 17 | ||||||
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ANDES Resource Report Resource Website 10+ mentions |
ANDES (RRID:SCR_002791) | data analysis software, data processing software, software application, software resource, software toolkit | Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses. | deep sequencing, biomarker detection, statistical analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20633290 | Free, Freely available, Available for download | biotools:andes, OMICS_01119 | https://bio.tools/andes | SCR_002791 | Statistical tools for the Analyses of Deep Sequencing (ANDES), Statistical tools for the Analyses of Deep Sequencing, Statistical tools for the ANalyses of Deep Sequencing | 2026-08-29 11:21:14 | 26 | ||||||
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GLProbs Resource Report Resource Website 1+ mentions |
GLProbs (RRID:SCR_002739) | software resource | Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:26357079 | Free, Freely available, Available for download | OMICS_03732 | SCR_002739 | 2026-08-29 11:21:19 | 1 | ||||||||
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Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow, https://sources.debian.org/src/bio-rainbow/ | SCR_002724 | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2026-08-29 11:21:11 | 41 | ||||||
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rDock Resource Report Resource Website 100+ mentions |
rDock (RRID:SCR_002838) | software resource | A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24722481 | Free, Freely available, Available for download | OMICS_03835 | SCR_002838 | 2026-08-29 11:21:20 | 122 | ||||||||
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FAS-DPD Resource Report Resource Website |
FAS-DPD (RRID:SCR_003068) | FAS-DPD | software resource | Software program to design degenerate primers for PCR. | command-line, java, primer, pcr, degenerate primer |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533783 | Free, Available for download, Freely available | OMICS_02340 | SCR_003068 | family-specific degenerate primer design | 2026-08-29 11:21:41 | 0 | ||||||
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GMcloser Resource Report Resource Website 1+ mentions |
GMcloser (RRID:SCR_000646) | GMcloser | software resource | Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:26261222 | Free, Available for download, Freely available | biotools:gmcloser, OMICS_00042 | https://bio.tools/gmcloser | SCR_000646 | Gmcloser - Closing the gaps in scaffolds with preassembled contigs | 2026-08-29 11:20:33 | 3 | |||||
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detecttd Resource Report Resource Website |
detecttd (RRID:SCR_000681) | detecttd | software resource | Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone. | tandem duplication, sequencing read, python, next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00315 | SCR_000681 | detecttd - Tool to detect tandem duplications in NGS reads | 2026-08-29 11:20:29 | 0 | |||||||
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FastUniq Resource Report Resource Website 1+ mentions |
FastUniq (RRID:SCR_000682) | software resource | A software tool for removal of de novo duplicates in paired short DNA sequences. | de novo, dna, sequence, duplicate, |
is listed by: OMICtools has parent organization: SourceForge |
DOI:10.1371/journal.pone.0052249 | Free, Available for download, Freely available | OMICS_01044 | SCR_000682 | 2026-08-29 11:20:34 | 4 | ||||||||
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TriageTools Resource Report Resource Website |
TriageTools (RRID:SCR_000675) | TriageTools | software resource | A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets. | matlab, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23408855 | Free, Available for download, Freely available | biotools:triagetools, nlx_156740 | https://bio.tools/triagetools | SCR_000675 | 2026-08-29 11:20:45 | 0 | ||||||
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NGS tools for the novice Resource Report Resource Website 1+ mentions |
NGS tools for the novice (RRID:SCR_000664) | NGS tools for the novice | software resource | A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution. | next generation sequencing, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01063 | SCR_000664 | NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data | 2026-08-29 11:20:44 | 3 | |||||||
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Opera Resource Report Resource Website 1+ mentions |
Opera (RRID:SCR_000665) | software resource | A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads. | sequence assembly, paired-end, orient contigs, shotgun-sequencing, shotgun, software program, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:27169502 PMID:21929371 |
Free, Available for download, Freely available | biotools:opera, OMICS_00045 | https://bio.tools/opera | SCR_000665 | OPERA-LG, Optimal Paired-End Read Assembler | 2026-08-29 11:20:29 | 3 | ||||||
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AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | 2026-08-29 11:20:42 | 0 | |||||||
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PHACCS Resource Report Resource Website 1+ mentions |
PHACCS (RRID:SCR_001232) | software resource | Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15743531 | Free, Available for download, Freely available | OMICS_03529 | SCR_001232 | 2026-08-29 11:20:47 | 1 | ||||||||
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QUAST Resource Report Resource Website 1000+ mentions |
QUAST (RRID:SCR_001228) | QUAST | software resource | Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots. | genome assembly, genomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Saint Petersburg Academic University; Saint Petersburg; Russia has parent organization: SourceForge |
PMID:23422339 | biotools:quast, OMICS_02115 | https://bio.tools/quast, https://sources.debian.org/src/quast/ | SCR_001228 | QUAST: Quality Assessment Tool for Genome Assemblies | 2026-08-29 11:21:00 | 3293 | ||||||
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Mutascope Resource Report Resource Website 1+ mentions |
Mutascope (RRID:SCR_001265) | Mutascope | data analysis software, data processing software, software application, software resource | Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations. | high throughput sequencing, pcr amplicon, pcr, mutation, amplicon, sequencing, somatic variant |
is listed by: OMICtools has parent organization: SourceForge |
Tumor, Normal | PMID:23712659 | Free, Public | OMICS_02074 | SCR_001265 | Mutascope - Analysis software designed for PCR-amplicon sequencing data | 2026-08-29 11:20:48 | 4 |
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