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biosymphony-antismash-cookbook.md

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antiSMASH 8 public integration guide

Status: checked baseline 8.0.4 for bacterial and fungal BGC calling.

antiSMASH does not provide the current plant-specific route in this kit. Use plantiSMASH for plant-focused calling and treat cross-tool agreement as supporting evidence rather than a substitute for biological review.

Input contract

Use a public or synthetic GenBank record with stable identifiers and appropriate feature annotations. Record the source accession, access date, input hash, taxon setting, antiSMASH version, database versions, and command.

Container pattern

Prefer the official, immutable image digest or a reproducibly built image. Verify the image source and database setup before use.

antismash \
  --taxon <BACTERIA_OR_FUNGI> \
  --output-dir <OUTPUT_DIR> \
  <INPUT_GENBANK>

Choose options from the current antiSMASH documentation rather than copying unreviewed historical flags.

Output contract

Retain:

  • the input accession and SHA-256;
  • the exact antiSMASH and database versions;
  • the full command and exit state;
  • region identifiers and coordinates;
  • compact JSON or tabular summaries;
  • hashes of retained outputs;
  • warnings and incomplete database states.

Raw inputs, large database payloads, provider logs, credentials, and provider response JSON stay outside this repository.

Review limits

A predicted region is a computational BGC hypothesis. Review gene models, domain evidence, neighborhood context, assembly quality, and supporting literature before making pathway or functional claims.

Sources: antiSMASH releases, documentation, and plantiSMASH.