1. 去除接头

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. 质控

mkdir -p fastqc
ls *.fq.gz|while read id;
do
fastqc -t 2 $id -o ./fastqc; 
done

3.spades组装

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