原创力文档- 1、本文档共36页，可阅读全部内容。
- 2、原创力文档（book118）网站文档一经付费（服务费），不意味着购买了该文档的版权，仅供个人/单位学习、研究之用，不得用于商业用途，未经授权，严禁复制、发行、汇编、翻译或者网络传播等，侵权必究。
- 3、本站所有内容均由合作方或网友上传，本站不对文档的完整性、权威性及其观点立场正确性做任何保证或承诺！文档内容仅供研究参考，付费前请自行鉴别。如您付费，意味着您自己接受本站规则且自行承担风险，本站不退款、不进行额外附加服务；查看《如何避免下载的几个坑》。如果您已付费下载过本站文档，您可以点击 这里二次下载。
- 4、如文档侵犯商业秘密、侵犯著作权、侵犯人身权等，请点击“版权申诉”（推荐），也可以打举报电话：400-050-0827(电话支持时间：9:00-18:30)。
ManualReferencePages-bwa
NAME
bwa-Burrows-WheelerAlignmentTool
CONTENTS
(1)Synopsis
(2)Description
(3)CommandsAndOptions
(4)SamAlignmentFormat
(5)NotesOnShort-readAlignment
AlignmentAccuracy
EstimatingInsertSizeDistribution
MemoryRequirement
Speed
(6)ChangesInBwa-0.6
(7)LicenseAndCitation
SYNOPSIS
bwaindexref.fa
bwamemref.fareads.fqaln-se.sam
bwamemref.faread1.fqread2.fqaln-pe.sam
bwaalnref.fashort_read.fqaln_sa.sai
bwasamseref.faaln_sa.saishort_read.fqaln-se.sam
bwasamperef.faaln_sa1.saialn_sa2.sairead1.fqread2.fqaln-pe.sam
bwabwaswref.falong_read.fqaln.sam
DESCRIPTION
BWAisasoftwarepackageformappinglow-divergentsequencesagainstalargereferencegenome,suchasthehumangenome.Itconsistsofthreealgorithms:BWA-backtrack,BWA-SWandBWA-MEM.ThefirstalgorithmisdesignedforIlluminasequencereadsupto100bp,whiletheresttwoforlongersequencesrangedfrom70bpto1Mbp.BWA-MEMandBWA-SWsharesimilarfeaturessuchaslong-readsupportandsplitalignment,butBWA-MEM,whichisthelatest,isgenerallyrecommendedforhigh-qualityqueriesasitisfasterandmoreaccurate.BWA-MEMalsohasbetterperformancethanBWA-backtrackfor70-100bpIlluminareads.
Forallthealgorithms,BWAfirstneedstoconstructtheFM-indexforthereferencegenome(theindexcommand).Alignmentalgorithmsareinvokedwithdifferentsub-commands:aln/samse/sampeforBWA-backtrack,bwaswforBWA-SWandmemfortheBWA-MEMalgorithm.
COMMANDSANDOPTIONS
index bwaindex[-pprefix][-aalgoType]in.db.fasta
IndexdatabasesequencesintheFASTAformat.
OPTIONS:
-pSTR Prefixoftheoutputdatabase[sameasdbfilename]
-aSTR AlgorithmforconstructingBWTindex.Availableoptionsare:
is ISlinear-timealgorithmforconstructingsuffixarray.Itrequires5.37NmemorywhereNisthesizeofthedatabase.ISismoderatelyfast,butdoesnotworkwithdatabaselargerthan2GB.
文档评论（0）