Using local BLAST

What BLAST is used for (in this workflow)

BLAST is optional and is used as an exploration tool:

  • For each inferred haplotype, the pipeline can query a local nucleotide BLAST database.

  • Results are summarized in <prefix>_blast.tsv and optionally included in the PDF report.

Warning

BLAST hits are not treated as an automatic species identification criterion. They are intended to help you compare haplotypes to your own curated reference set.

Install BLAST+

You need the BLAST+ executables, typically:

  • blastn

  • makeblastdb (only required if you need to build a DB from FASTA)

Prepare a database

If you already have a formatted BLAST DB, place it in:

blast/HmtG_database_PacBio.*

If you want to build a DB from a FASTA file:

makeblastdb -in HmtG_database_PacBio.fasta -dbtype nucl -out blast/HmtG_database_PacBio

Run and verify

After a run, look for:

  • <prefix>_blast.tsv

If the file is missing, check FAQ / Troubleshooting (common causes: BLAST not found, DB prefix incorrect).