软件1、cutadapt

input=test.fq.gz

mkdir -p cutadapt

cutadapt_input=$input

cutadapt_out=cutadapt/trimed.fastq.gz

interleaved=--interleaved

cutadapt $interleaved -a AGATCGGAAGAGC -A AGATCGGAAGAGC -q 30 -m 20 --trim-n -O 10 -o $cutadapt_out $cutadapt_input

软件2、megahit

input_fa=$cutadapt_out

assembly_out=assembly_out

megahit --12 $input_fa --k-max 149 --max-tip-len 200 --min-contig-len 300 -o $assembly_out

软件3、MetaGeneMark

mkdir -p predict_gene

input_dir=assembly_out

predict_gene_out=predict_gene

model_file=../MetaGeneMark_linux_64/mgm/MetaGeneMark_v1.mod

cp ../MetaGeneMark_linux_64/gm_key ~/.gm_key

gmhmmp -d -f G -m $model_file -o $predict_gene_out/out.gff -A $predict_gene_out/final.prot.fa -D $predict_gene_out/final.nucl.fa $input_dir/final.contigs.fa

软件4、cd-hit<