利用二代数据对三代基因组纠错2021-01-22

一、polish 软件安装
https://github.com/broadinstitute/pilon/releases下直接下载pilon-1.23.jar
java -Xmx16G -jar pilon-1.23.jar 直接使用。

二、二代数据比对
第一次 polish

#! /bin/sh
bwa index  prefix3.fa
bwa mem -t 12 prefix3.fa ../data/ziye_1.fastq ../data/ziye_2.fastq | ~/usr/bin/samtools_1.9 view -Sb - > align1.bam
~/usr/bin/samtools_1.9 sort -@ 12 -o align1.sorted.bam align1.bam
~/usr/bin/samtools_1.9 index -@ 12 align1.sorted.bam
sambamba markdup -t 12 align1.sorted.bam align1.sorted.markup.bam
rm align1.bam align1.sorted.bam
~/usr/bin/samtools_1.9 view  -@ 12 -q 30 -b align1.sorted.markup.bam >align1.sorted.markup.filter.bam
~/usr/bin/samtools_1.9 index -@ 12 align1.sorted.markup.filter.bam
java -Xmx480G -jar ~/usr/pilon-1.23.jar --genome  prefix3.fa --frags align1.sorted.markup.filter.bam --fix snps,indels --output pilon_polished1

第二次 polish

#! /bin/sh
bwa index  pilon_polished1.fasta
bwa mem -t 12 pilon_polished1.fasta ../data/ziye_1.fastq ../data/ziye_2.fastq | ~/usr/bin/samtools_1.9 view -Sb - > align2.bam
~/usr/bin/samtools_1.9 sort -@ 12 -o align2.sorted.bam align2.bam
~/usr/bin/samtools_1.9 index -@ 12 align2.sorted.bam
sambamba markdup -t 12 align2.sorted.bam align2.sorted.markup.bam
rm align2.bam align2.sorted.bam
~/usr/bin/samtools_1.9 view  -@ 12 -q 30 -b align2.sorted.markup.bam >align2.sorted.markup.filter.bam
~/usr/bin/samtools_1.9 index -@ 12 align2.sorted.markup.filter.bam
java -Xmx480G -jar ~/usr/pilon-1.23.jar --genome  pilon_polished1.fasta --frags align2.sorted.markup.filter.bam --fix snps,indels --output pilon_polished2

参考：

https://www.jianshu.com/p/cceeb7d1f413
https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage