NBISweden / Earth-Biogenome-Project-pilot

Assembly and Annotation workflows for analysing data in the Earth Biogenome Project pilot project.
https://www.earthbiogenome.org/
GNU General Public License v3.0
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New Module: PREP_HIFI #2

Closed aersoares81 closed 2 years ago

aersoares81 commented 2 years ago

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
mahesh-panchal commented 2 years ago

Implemented in SAMTOOLS_FASTA