BWA操作手册.docx

Manual Reference Pages - bwaNAMEbwa - Burrows-Wheeler Alignment ToolCONTENTS(1) Synopsis(2) Description(3) Commands And Options(4) Sam Alignment Format(5) Notes On Short-read Alignment Alignment Accuracy Estimating Insert Size Distribution Memory Requirement Speed(6) Changes In Bwa-0.6(7) License And CitationSYNOPSISbwa index ref.fabwa mem ref.fa reads.fq aln-se.sambwa mem ref.fa read1.fq read2.fq aln-pe.sambwa aln ref.fa short_read.fq aln_sa.saibwa samse ref.fa aln_sa.sai short_read.fq aln-se.sambwa sampe ref.fa aln_sa1.sai aln_sa2.sai read1.fq read2.fq aln-pe.sambwa bwasw ref.fa long_read.fq aln.samDESCRIPTIONBWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp. BWA-MEM and BWA-SW share similar features such as long-read support and split alignment, but BWA-MEM, which is the latest, is generally recommended for high-quality queries as it is faster and more accurate. BWA-MEM also has better performance than BWA-backtrack for 70-100bp Illumina reads.For all the algorithms, BWA first needs to construct the FM-index for the reference genome (the index command). Alignment algorithms are invoked with different sub-commands: aln/samse/sampe for BWA-backtrack, bwasw for BWA-SW and mem for the BWA-MEM algorithm.COMMANDS AND OPTIONSindexbwa index [-p prefix] [-a algoType] in.db.fastaIndex database sequences in the FASTA format.OPTIONS:-p STRPrefix of the output database [same as db filename]-a STRAlgorithm for constructing BWT index. Available options are:isIS linear-time algorithm for constructing suffix array. It requires 5.37N memory where N is the size of the database. IS is moderately fast, but does not work with database larger than 2GB. IS is the default algorithm due to its simplicity. The