BWA DNA mapping工具
BWA 全名 Burrow-Wheeler Aligner,是一款将DNA序列mapping到参考基因组上的软件
下载地址
准备工作
yum groupinstall -y 'Development Tools'
yum install -y zlib.x86_64 zlib-devel.x86_64
编译
tar jxvf bwa-0.7.17.tar.bz2
cd bwa-0.7.17
make -j 8
环境变量
echo 'export PATH=/opt/bwa-0.7.17:$PATH' >> /etc/profile
source /etc/profile
查看说明
[root@localhost bwa-0.7.17]# ./bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
Contact: Heng Li <lh3@sanger.ac.uk>
Usage: bwa <command> [options]
Command: index index sequences in the FASTA format
mem BWA-MEM algorithm
fastmap identify super-maximal exact matches
pemerge merge overlapping paired ends (EXPERIMENTAL)
aln gapped/ungapped alignment
samse generate alignment (single ended)
sampe generate alignment (paired ended)
bwasw BWA-SW for long queries
shm manage indices in shared memory
fa2pac convert FASTA to PAC format
pac2bwt generate BWT from PAC
pac2bwtgen alternative algorithm for generating BWT
bwtupdate update .bwt to the new format
bwt2sa generate SA from BWT and Occ
Note: To use BWA, you need to first index the genome with `bwa index'.
There are three alignment algorithms in BWA: `mem', `bwasw', and
`aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
first. Please `man ./bwa.1' for the manual.
使用示例:
# 建索引
bwa index -a bwtsw -p hg19 hg19.fa 1>hg19.bwa_index.log 2>&1
# 比对 t为线程数量
bwa mem -t 8 -M -R @RG\tID:KPGP-00001_L1\tSM:KPGP-00001_L1\tLB:WGS\tPL:Illumina ~/reference/index/bwa/hg19 KPGP-00001_L1_R1.fq.gz KPGP-00001_L1_R2.fq.gz 1>KPGP-00001_L1.sam 2>KPGP-00001_L1.bwa.align.log
[root@localhost ~]# bwa index E.coli_K12_MG1655.fa
[bwa_index] Pack FASTA... 0.04 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 1.74 seconds elapse.
[bwa_index] Update BWT... 0.03 sec
[bwa_index] Pack forward-only FASTA... 0.02 sec
[bwa_index] Construct SA from BWT and Occ... 0.69 sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa index E.coli_K12_MG1655.fa
[main] Real time: 2.546 sec; CPU: 2.534 sec
[root@localhost ~]# ls -l
-rw-r--r--. 1 root root 4699745 Nov 9 22:05 E.coli_K12_MG1655.fa
-rw-r--r--. 1 root root 12 Nov 10 00:03 E.coli_K12_MG1655.fa.amb
-rw-r--r--. 1 root root 98 Nov 10 00:03 E.coli_K12_MG1655.fa.ann
-rw-r--r--. 1 root root 4641732 Nov 10 00:03 E.coli_K12_MG1655.fa.bwt
-rw-r--r--. 1 root root 29 Nov 9 22:45 E.coli_K12_MG1655.fa.fai
-rw-r--r--. 1 root root 1160415 Nov 10 00:03 E.coli_K12_MG1655.fa.pac
-rw-r--r--. 1 root root 2320880 Nov 10 00:03 E.coli_K12_MG1655.fa.sa