bwa的安装与使用

bwa的安装与使用BWA安装流程安装本软体总共需要完成以下两个软体的安装工作 BWA SamtoolBWA安装下载BWA (download from BWA Source Forge ) bwa-0.5.7.tar.bz2 安装BWA# tar -jxvf bwa-0.5.7.tar.bz2编译BWA# makeSamtool安装下载Samtool (download from Samtool Source Forge )安装Samtool# tar -jxvf samtools-*.tar.bz2# makeBWA使用流程1.Index the database file in the FASTA format2.Find the suffix array (SA) coordinates of good hits of each individual read3.Convert SA coordinates to chromosomal coordinate and pair reads准备资料Reference genome data (*.fa)NGS Short reads data (*.fastq)建立Index根据reference genome data(eg reference.fa) 建立Index File# bwa index -a bwtsw reference.fa若是资料是colorspace 的话，就要建立colorspace 的index file#./bwa index -a bwtsw -c reference.fabwa index 指令更多的用法及options#./bwa index参数说明* -c ：建立colorspace的index所需要的参数。寻找SA coordinates利用以下资料找SA coordinatesNGS short reads data (eg leftRead.fastq / rightRead.fastq)refernece genome data(eg reference.fa)# bwa aln reference.fa leftRead.fastq leftRead.sai# bwa aln reference.fa rightRead.fastq rightRead.sai若是资料是colorspace 的话,则必须先使用内附的solid2fastq.pl 档案先行转换reads，再产生SA coordinates ，指令如下#./bwa aln -c -f leftreads.sai reference.fa leftreads.fastq#./bwa aln -c -f rightreads.sai reference.fa rightreads.fastq若是希望使用multi threads 跑指令的话#./bwa aln -c -t 3 -f leftreads.sai reference.fa leftreads.fastqbwa aln 指令更多的用法及options#./bwa aln参数说明* -f file：file to write output to instead of stdout* -c：input sequences are in the color space* -t num ：number of threads. (初始值：1)转换SA coordinates利用以下资料转换SA coordinates file 输出Sam file# bwa sampe reference.fa leftRead.sai rightRead.sai leftRead.fastq rightread.fastq human.samGenerate alignments in the SAM format given single-end reads#./bwa samse -f leftreads.sam reference.fa leftreads.sai leftreads.fastq#./bwa samse -f rightreads.sam reference.fa rightreads.sai rightreads.fastq让结果出现有multiple mapped 的相关内容#./bwa samse -n 10000 -f leftreads.sam reference.fa leftreads.sai leftreads.fastq更多bwa sampe 和bwa samse 的指令用法和相关的options#./bwa sampe#./bwa samse参数说明* -f fi