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 - Domain and family annotation
• eggNOG-mapper - Orthology-based functional annotation
• DIAMOND - Fast sequence homology search
• TaxonKit - Taxonomy resolution and manipulation

References

• See ../bio-skills-references.md