Hollyhlp

And here is the command I used: coverm genome --coupled /data3/final_pure_reads_1.fastq /data3//final_pure_reads_2.fastq --genome-fasta-directory /data3/HLP/srenamed/ -o B-DNA-abundance/B0-count -m count --min-read-aligned-percent 0.75 --min-read-percent-identity 0.95 --min-covered-fraction 0 -p bwa-mem -t 90