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Research · Data Analysis / AGENT SKILL
bio-annotation
0
Infer biological function and taxonomy from sequence homology.
Functional annotation and taxonomy inference from sequence homology.
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Original instructions from the publisher’s SKILL.md
# Bio Annotation ## When to use - Functional annotation and taxonomy inference from sequence homology. ## Prerequisites - Tools installed via pixi (see pixi.toml). - Reference DB root: /media/shared-expansion/db/ (wsu; override per machine branch). - Input FASTA and reference DBs are readable. ## Inputs - proteins.faa (FASTA protein sequences). - reference_db/ (eggNOG, InterPro, DIAMOND databases + taxdump). ## Outputs - results/bio-annotation/annotations.parquet - results/bio-annotation/taxonomy.parquet - results/bio-annotation/annotation_report.md - results/bio-annotation/logs/ ## Steps 1. Run InterProScan for domain/family annotation. 2. Run eggnog-mapper for orthology-based annotation. 3. Run DIAMOND and resolve taxonomy with TaxonKit. ## QC gates - Annotation hit rate and taxonomy rank coverage meet project thresholds. - On failure: retry with alternative parameters; if still failing, record in report and exit non-zero. ## Validation - Verify proteins.faa is non-empty and amino acid encoded. - Verify required reference DBs exist under the reference root. ## Tools - interproscan v6.0.0 - eggnog-mapper v2.1.13 - diamond v2.1.16 - taxonkit v0.20.0 ## Paper summaries (2023-2025) - summaries/ (include example use cases and tool settings used) ## Tool documentation - [InterProScan](docs/interproscan.html) - Domain and family annotation - [eggNOG-mapper](docs/eggnog-mapper.html) - Orthology-based functional annotation - [DIAMOND](docs/diamond-usage.md) - Fast sequence homology search - [TaxonKit](docs/taxonkit.html) - Taxonomy resolution and manipulation ## References - See ../bio-skills-references.md