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1. 去除接頭
1.1 fastp
ls *.fastq.gz|while read id;
do
fastp -a CTGTCTCTTATA -5 30 -3 30 -i $id -o ${id%%.*}.clean.fq.gz -h ./fastp/${id%%.*}.html -j ./fastp/${id%%.*}.json;
done
1.2 cutadapt
conda install -c bioconda cutadapt
ls *.fastq.gz|while read id;
do
cutadapt -a CTGTCTCTTATACACATCT -e 0.2 -o ${id%%.*}.clean.fq.gz $id
done
2. 質(zhì)控
mkdir -p fastqc
ls *.fq.gz|while read id;
do
fastqc -t 2 $id -o ./fastqc;
done
3.spades組裝
ls *.fq.gz|while read id;
do
spades.py --plasmid -k 39, 41,71,75,77 -s $id -o ./${id%_*} -t 2 --cov-cutoff auto --careful
done
spades.py --plasmid -k 39,41,77 -s 71112159116_S119_L001_R1_001.clean.fq.gz -o ./spades_assemble -t 2 --cov-cutoff auto --careful
