The HiFi reads come in a BAM file, which is not easily parsed downstream, so converting to FASTA.
originally:
#!/usr/bin/env bash
module load bioinfo-tools samtools
output=/where/to/write
while read name read; do
samtools fasta "${read}" > "${output}/${name}.fasta"
done < list.tab
The HiFi reads come in a BAM file, which is not easily parsed downstream, so converting to FASTA.
originally: