二代测序数据分析软件包大全.docx
- 文档编号:10462557
- 上传时间:2023-02-13
- 格式:DOCX
- 页数:14
- 大小:407.84KB
二代测序数据分析软件包大全.docx
《二代测序数据分析软件包大全.docx》由会员分享,可在线阅读,更多相关《二代测序数据分析软件包大全.docx(14页珍藏版)》请在冰豆网上搜索。
二代测序数据分析软件包大全
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.
* Galaxy -Galaxy=interactiveandreproduciblegenomics.Ajobwebportal.
* Genomatix -IntegratedSolutionsforNextGenerationSequencingdataanalysis.
* JMPGenomics -NextgenvisualizationandstatisticstoolfromSAS.Theyare workingwithNCGR torefinethistoolandproduceothers.
* NextGENe - denovo andreferenceassemblyofIllumina,SOLiDandRocheFLXdata.UsesanovelCondensationAssemblyToolapproachwherereadsarejoinedvia"anchors"intomini-contigsbeforeassembly.IncludesSNPdetection,CHiP-seq,browserandotherfeatures.Commercial.WinorMacOS.
* SeqManGenomeAnalyser -SoftwareforNextGenerationsequenceassemblyofIllumina,RocheFLXandSangerdataintegratingwithLasergeneSequenceAnalysissoftwareforadditionalanalysisandvisualizationcapabilities.Canuseahybridtemplated/denovoapproach.Commercial.WinorMacOSX.
* SHORE -SHORE,forShortRead,isamappingandanalysispipelineforshortDNAsequencesproducedonaIlluminaGenomeAnalyzer.Asuitecreatedbythe1001Genomesproject.SourceforPOSIX.
* SlimSearch -Fledglingcommercialproduct.
Align/Assembletoareference
* BFAST -Blat-likeFastAccurateSearchTool.WrittenbyNilsHomer,StanleyF.NelsonandBarryMerrimanatUCLA.
* Bowtie -Ultrafast,memory-efficientshortreadaligner.ItalignsshortDNAsequences(reads)tothehumangenomeatarateof25millionreadsperhouronatypicalworkstationwith2gigabytesofmemory.UsesaBurrows-Wheeler-Transformed(BWT)index. Linktodiscussionthreadhere.WrittenbyBenLangmeadandColeTrapnell.Linux,Windows,andMacOSX.
* BWA -HengLee'sBWTAlignmentprogram-aprogressionfromMaq.BWAisafastlight-weightedtoolthatalignsshortsequencestoasequencedatabase,suchasthehumanreferencegenome.Bydefault,BWAfindsanalignmentwithineditdistance2tothequerysequence.C++source.
* ELAND -EfficientLarge-ScaleAlignmentofNucleotideDatabases.Wholegenomealignmentstoareferencegenome.WrittenbyIlluminaauthorAnthonyJ.CoxfortheSolexa1Gmachine.
* Exonerate -Variousformsofpairwisealignment(includingSmith-Waterman-Gotoh)ofDNA/proteinagainstareference.AuthorsareGuyStCSlaterandEwanBirneyfromEMBL.CforPOSIX.
* GenomeMapper -GenomeMapperisashortreadmappingtooldesignedforaccuratereadalignments.Itquicklyalignsmillionsofreadseitherwithungappedorgappedalignments.Atoolcreatedbythe1001Genomesproject.SourceforPOSIX.
* GMAP -GMAP(GenomicMappingandAlignmentProgram)formRNAandESTSequences.DevelopedbyThomasWuandColinWatanabeatGenentec.C/PerlforUnix.
* gnumap -TheGenomicNext-generationUniversalMAPper(gnumap)isaprogramdesignedtoaccuratelymapsequencedataobtainedfromnext-generationsequencingmachines(specificallythatofSolexa/Illumina)backtoagenomeofanysize.Itseekstoalignreadsfromnonuniquerepeatsusingstatistics.FromauthorsatBrighamYoungUniversity.Csource/Unix.
* MAQ -MappingandAssemblywithQualities(renamedfromMAPASS2).ParticularlydesignedforIlluminawithpreliminaryfunctionstohandleABISOLiDdata.WrittenbyHengLifromtheSangerCentre.FeaturesextensivesupportingtoolsforDIP/SNPdetection,etc.C++source
* MOSAIK -MOSAIKproducesgappedalignmentsusingtheSmith-Watermanalgorithm.Featuresanumberofsupporttools.SupportforRocheFLX,Illumina,SOLiD,andHelicos.WrittenbyMichaelStr?
mbergatBostonCollege.Win/Linux/MacOSX
* MrFASTandMrsFAST -mrFAST&mrsFASTaredesignedtomapshortreadsgeneratedwiththeIlluminaplatformtoreferencegenomeassemblies;inafastandmemory-efficientmanner.RobusttoINDELsandMrsFASThasabisulphitemode.AuthorsarefromtheUniversityofWashington.Cassource.
* MUMmer -MUMmerisamodularsystemfortherapidwholegenomealignmentoffinishedordraftsequence.Releasedasapackageprovidinganefficientsuffixtreelibrary,seed-and-extendalignment,SNPdetection,repeatdetection,andvisualizationtools.Version3.0wasdevelopedbyStefanKurtz,AdamPhillippy,ArthurLDelcher,MichaelSmoot,MartinShumway,CorinaAntonescuandStevenLSalzberg-mostofwhomareatTheInstituteforGenomicResearchinMaryland,USA.POSIXOSrequired.
* Novocraft -Toolsforreferencealignmentofpaired-endandsingle-endIlluminareads.UsesaNeedleman-Wunschalgorithm.CansupportBis-Seq.Commercial.Availablefreeforevaluation,educationaluseandforuseonopennot-for-profitprojects.RequiresLinuxorMacOSX.
* PASS -ItsupportsIllumina,SOLiDandRoche-FLXdataformatsandallowstheusertomodulateveryfinelythesensitivityofthealignments.Spacedseedintialfilter,thenNWdynamicalgorithmtoaSW(like)localalignment.AuthorsarefromCRIBIinItaly.Win/Linux.
* RMAP -Assembles20-64bpIlluminareadstoaFASTAreferencegenome.ByAndrewD.SmithandZhenyuXuanatCSHL.(publishedinBMCBioinformatics).POSIXOSrequired.
* SeqMap -Supportsupto5ormorebpmismatches/INDELs.Highlytunable.WrittenbyHuiJiangfromtheWonglabatStanford.BuildsavailableformostOS's.
* SHRiMP -Assemblestoareferencesequence.DevelopedwithAppliedBiosystem'scolourspacegenomicrepresentationinmind.AuthorsareMichaelBrudnoandStephenRumbleattheUniversityofToronto.POSIX.
* Slider-AnapplicationfortheIlluminaSequenceAnalyzeroutputthatusestheprobabilityfilesinsteadofthesequencefilesasaninputforalignmenttoareferencesequenceorasetofreferencesequences.AuthorsarefromBCGSC.Paperis here.
* SOAP -SOAP(ShortOligonucleotideAlignmentProgram).Aprogramforefficientgappedandungappedalignmentofshortoligonucleotidesontoreferencesequences.TheupdatedversionusesaBWT.CancallSNPsandINDELs.AuthorisRuiqiangLiattheBeijingGenomicsInstitute.C++,POSIX.
* SSAHA -SSAHA(SequenceSearchandAlignmentbyHashingAlgorithm)isatoolforrapidlyfindingnearexactmatchesinDNAorproteindatabasesusingahashtable.DevelopedattheSangerCentrebyZeminNing,AnthonyCoxandJamesMullikin.C++forLinux/Alpha.
* SOCS -AlignsSOLiDdata.SOCSisbuiltonaniterativevariationoftheRabin-Karpstringsearchalgorithm,whichuseshashingtoreducethesetofpossiblematches,drasticallyincreasingsearchspeed.AuthorsareOndovB,VaradarajanA,PassalacquaKDandBergmanNH.
* SWIFT -TheSWIFTsuitisasoftwarecollectionforfastindex-basedsequencecomparison.Itcontains:
SWIFT—fastlocalalignmentsearch,guaranteeingtofindepsilon-matchesbetweentwosequences.SWIFTBALSAM—averyfastprogramtofindsemiglobalnon-gappedalignmentsbasedonk-merseeds.AuthorsareKimRasmussen(SWIFT)andWolfgangGerlach(SWIFTBALSAM)
* SXOligoSearch -SXOligoSearchisacommercialplatformofferedbytheMalaysianbased Synamatix.WillalignIlluminareadsagainstarangeofRefseqRNAorNCBIgenomebuildsforanumberoforganisms.WebPortal.OSindependent.
* Vmatch -Aversatilesoftwaretoolforefficientlysolvinglargescalesequencematchingtasks.VmatchsubsumesthesoftwaretoolREPuter,butismuchmoregeneral,withaveryflexibleuserinterface,andimprovedspaceandtimerequirements.Essentiallyalargestringmatchingtoolbox.POSIX.
* Zoom -ZOOM(ZillionsOfOligosMapped)isdesignedtomapmillionsofshortreads,emergedbynext-generationsequencingtechnology,backtothereferencegenomes,andcarryoutpost-analysis.ZOOMisdevelopedtobehighlyaccurate,flexible,anduser-friendlywithspeedbeingacriticalpriority.Commercial.SupportsIlluminaandSOLiDdata.
Denovo Align/Assemble
* ABySS -AssemblyByShortSequences.ABySSisadenovosequenceassemblerthatisdesignedforveryshortreads.Thesingle-processorversionisusefulforassemblinggenomesupto40-50Mbasesinsize.TheparallelversionisimplementedusingMPIandiscapableofassemblinglargergenomes.BySimpsonJTandothersattheCanada'sMichaelSmithGenomeSciencesCentre.C++assource.
* ALLPATHS -ALLPATHS:
Denovoassemblyofwhole-genomeshotgunmicroreads.ALLPATHSisawholegenomeshotgunassemblerthatcangeneratehighqualityassembliesfromshortreads.Assembliesarepresentedinagraphformthatretainsambiguities,suchasthosearisingfrompolymorphism,therebyprovidinginformationthathasbeenabsentfrompreviousgenomeassemblies.BroadInstitute.
* Edena -Edena(ExactDENovoAssembler)isanassemblerdedicatedtoprocessthemillionsofveryshortreadsproducedbytheIlluminaGenomeAnalyzer.Edenaisbasedonthetraditionaloverlaplayoutparadigm.ByD.Hernandez,P.Fran?
ois,L.Farinelli,M.Osteras,andJ.Schrenzel.Linux/Win.
* EULER-SR -Shortread denovo assembly.ByMarkJ.ChaissonandPavelA.PevznerfromUCSD(publishedinGenomeResearch).UsesadeBruijngraphapproach.
* MIRA2 -MIRA(MimickingIntelligentReadAssembly)isabletoperformtruehybridde-novoassembliesusingreadsgatheredthrough454sequencingtechnology(GS20orGSFLX).Compatiblewith454,SolexaandSangerdata.LinuxOSrequired.
* SEQAN -AConsistency-basedConsensusAlgorithmforDeNovoandReference-guidedSequenceAssemblyofShortReads.ByTobiasRauschandothers.C++,Linux/Win.
* SHARCGS -Denovoassemblyofshortreads.AuthorsareDohmJC,LottazC,BorodinaTandHimmelbauerH.fromtheMax-Planck-InstituteforMolecularGenetics.
* SSAKE -TheShortSequence
- 配套讲稿:
如PPT文件的首页显示word图标,表示该PPT已包含配套word讲稿。双击word图标可打开word文档。
- 特殊限制:
部分文档作品中含有的国旗、国徽等图片,仅作为作品整体效果示例展示,禁止商用。设计者仅对作品中独创性部分享有著作权。
- 关 键 词:
- 二代 序数 分析 软件包 大全