shell-for循环处理宏基因组数据 - 2021-12-27

Megahit-宏基因组组装流程

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for i in XH*_1.fq.gz; do

I=${i%_*}_2.fq.gz

base=${i%%_*}.megahit

megahit -1 $i -2 $I --k-list 21,29,39,59,79,99,119,141 --min-contig-len 1000 -t 12 -o $base

done

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Prodigal-预测ORFs

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for i in prodigal/XH*.contigs.fa; do

file=${i#*/}

base=${file%%.*}.prodigal

mkdir $base

prodigal -i $i -a $base/$base.faa -d $base/$base.fna -p meta -o $base/$base.gbk

done

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刚踏入生信分析的环境硕士，此文仅为个人学习纪录。