2014
Population-based structural variation discovery with Hydra-Multi
Lindberg MR, Hall IM, Quinlan AR. Population-based structural variation discovery with Hydra-Multi. Bioinformatics 2014, 31: 1286-1289. PMID: 25527832, PMCID: PMC4393510, DOI: 10.1093/bioinformatics/btu771.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsDatabases, FactualGene DeletionGenetics, PopulationGenomic Structural VariationGenomicsHumansHydraSequence AlignmentSoftwareConceptsNumber of genomesSV analysisStructural variation discoveryStructural variant detectionHuman genomeCancer Genome AtlasVariation discoveryGenomic rearrangementsGenome ProjectSequence alignmentSignal integrationIndel discoveryGenome AtlasGenomeMultiple individualsSupplementary dataSize variabilityVariant detectionCommodity hardwarePoor scalabilityAvailable datasetsAnalysis workflowScalabilityExtant toolsDiscoverySAMBLASTER: fast duplicate marking and structural variant read extraction
Faust GG, Hall IM. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics 2014, 30: 2503-2505. PMID: 24812344, PMCID: PMC4147885, DOI: 10.1093/bioinformatics/btu314.Peer-Reviewed Original Research
2012
YAHA: fast and flexible long-read alignment with optimal breakpoint detection
Faust GG, Hall IM. YAHA: fast and flexible long-read alignment with optimal breakpoint detection. Bioinformatics 2012, 28: 2417-2424. PMID: 22829624, PMCID: PMC3463118, DOI: 10.1093/bioinformatics/bts456.Peer-Reviewed Original ResearchConceptsSingle best alignmentLinux systemQueriesAcyclic graphBWA-SWAlignment toolsSimple heuristicsMultiple mappingsOptimal setAssembly algorithmStructural variant detectionComplex SVsBreakpoint detectionPossible alignmentsSample dataSV classesYahaLess timeBetter alignmentVariant detectionAlignersDownloadHeuristicsSSAHA2Algorithm