Megahit-宏基因組組裝流程
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 $base
done
Prodigal-預(yù)測ORFs
for i in prodigal/XH*.contigs.fa; do
file=${i#*/}
base=${file%%.*}.prodigal
mkdir $base
prodigal -i $i -a $base/$base.faa -d $base/$base.fna -p meta -o $base/$base.gbk
done
剛踏入生信分析的環(huán)境碩士，此文僅為個(gè)人學(xué)習(xí)紀(jì)錄意荤。
