bowtie2-build contigs.fa fre
bowtie2 -p 32 -x fre -1 reads_1.fastq -2 reads_2.fastq -S Alignment.sam
samtools view -bS Alignment.sam > Alignment.bam
samtools sort Alignment.bam > Alignment.sort.bam
samtools index Alignment.sort.bam
java -Xmx16G -jar pilon-1.22.jar --genome contigs.fa --frags Alignment.sort.bam --fix snps,indels --output pilon_polished --vcf &> pilon.log
pilon 参数
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转载自blog.csdn.net/abcsmallxhj/article/details/83869735
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