bwa软件对参考基因组构建索引文件

 

1、当参考基因组

大于2G时（约20亿个核苷酸，20,0000,0000）：bwa index -a bwtsw  xxx.fa

小于2G时（约20亿个核苷酸，20,0000,0000）：bwa index xxx.fa

 

2、统计参考基因组碱基数目

root@DESKTOP-1N42TVH:/home/test# ls
Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
root@DESKTOP-1N42TVH:/home/test# grep -v "^>" Arabidopsis_thaliana.TAIR10.dna.toplevel.fa | awk 'BEGIN{sum = 0} {sum += length($0)} END {print sum}'
119667750

 

3、bwa对参考基因组构建索引，生成五个文件

root@DESKTOP-1N42TVH:/home/test# ls
Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
root@DESKTOP-1N42TVH:/home/test# bwa index Arabidopsis_thaliana.TAIR10.dna.toplevel.fa
root@DESKTOP-1N42TVH:/home/test# ls
Arabidopsis_thaliana.TAIR10.dna.toplevel.fa      Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.bwt
Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.amb  Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.pac
Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.ann  Arabidopsis_thaliana.TAIR10.dna.toplevel.fa.sa