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1、二代测序数据分析软件包大全Integratedsolutions* CLCbioGenomicsWorkbench - denovo andreferenceassemblyofSanger,RocheFLX,Illumina,Helicos,andSOLiDdata.Commercialnext-gen-seqsoftwarethatextendstheCLCbioMainWorkbenchsoftware.IncludesSNPdetection,CHiP-seq,browserandotherfeatures.Commercial.Windows,MacOSXandLinux.*
2、 Galaxy -Galaxy=interactiveandreproduciblegenomics.Ajobwebportal.* Genomatix -IntegratedSolutionsforNextGenerationSequencingdataanalysis.* JMPGenomics -NextgenvisualizationandstatisticstoolfromSAS.Theyare workingwithNCGR torefinethistoolandproduceothers.* NextGENe - denovo andreferenceassemblyof
3、Illumina,SOLiDandRocheFLXdata.UsesanovelCondensationAssemblyToolapproachwherereadsarejoinedvia"anchors"intomini-contigsbeforeassembly.IncludesSNPdetection,CHiP-seq,browserandotherfeatures.Commercial.WinorMacOS.* SeqManGenomeAnalyser -SoftwareforNextGenerationsequenceassemblyofIllumina,RocheFLXan
4、dSangerdataintegratingwithLasergeneSequenceAnalysissoftwareforadditionalanalysisandvisualizationcapabilities.Canuseahybridtemplated/denovoapproach.Commercial.WinorMacOSX.* SHORE -SHORE,forShortRead,isamappingandanalysispipelineforshortDNAsequencesproducedonaIlluminaGenomeAnalyzer.Asuitecreatedby
5、the1001Genomesproject.SourceforPOSIX.* SlimSearch -Fledglingcommercialproduct.Align/Assembletoareference* BFAST -Blat-likeFastAccurateSearchTool.WrittenbyNilsHomer,StanleyF.NelsonandBarryMerrimanatUCLA.* Bowtie -Ultrafast,memory-efficientshortreadaligner.ItalignsshortDNAsequences(reads)tothehuma
6、ngenomeatarateof25millionreadsperhouronatypicalworkstationwith2gigabytesofmemory.UsesaBurrows-Wheeler-Transformed(BWT)index. Linktodiscussionthreadhere.WrittenbyBenLangmeadandColeTrapnell.Linux,Windows,andMacOSX.* BWA -HengLee'sBWTAlignmentprogram-aprogressionfromMaq.BWAisafastlight-weightedtool
7、thatalignsshortsequencestoasequencedatabase,suchasthehumanreferencegenome.Bydefault,BWAfindsanalignmentwithineditdistance2tothequerysequence.C++source.* ELAND -EfficientLarge-ScaleAlignmentofNucleotideDatabases.Wholegenomeal
