A workflow for creating Virtool subtractions.
- Compute sequence count and nucleotide distribution using
seqkit. - Compress the FASTA file for upload and long term retention, if it isn't already compressed.
- Upload the FASTA to the Virtool server and add sequence count and nucleotide distribution data to the subtraction record.
seqkit reads gzip-compressed FASTA natively, so the workflow never decompresses the input file to
disk — this avoids the disk space blowup that comes from holding both the compressed input and a
decompressed copy for large subtraction FASTA files.
Bowtie2 indexes are not built here. Analysis workflows that need one build it locally from the subtraction FASTA.