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