CoverM：contig/bin的相对丰度计算

GitHub - wwood/CoverM: Read alignment statistics for metagenomics

 安装

mamba create -n coverm
mamba activate coverm
mamba install coverm
coverm -h

使用 

#!/bin/bash
source /home/zhongpei/miniconda3/bin/activate covermcd /home/zhongpei/diarrhoea/MJ/Data/CleanData
for i in *_clean_2.fastq.gz
donum=${i%%_clean_2.fastq.gz}coverm genome --coupled ${num}_clean_1.fastq.gz ${num}_clean_2.fastq.gz --genome-fasta-directory /home/zhongpei/diarrhoea/MJ/Data/Bin_benfen/bin_quality/ --genome-fasta-extension fa \-t 24  -m tpm relative_abundance covered_fraction  -o /home/zhongpei/diarrhoea/MJ/Data/Bin_benfen/coverm_result/${num}_bin_quality_coverm.tsv
done