AnnotationQC

Snakemake workflow to generate QC metric tables for gff3 or gtf formatted genome annotation files.

Metrics

• Completeness (BUSCO) — assessed with compleasm at both the protein and transcript level. The completeness score is

  busco_score = 1 - (missing / total)
  

  where missing is the number of Missing BUSCOs and total is the number of BUSCOs in the lineage database. Protein level runs compleasm protein; transcript level runs compleasm run on the extracted transcript FASTA (miniprot aligns the BUSCO orthologs to the transcripts).

Additional metric families (structural counts, feature-length distributions, coding-integrity / UTR checks) will be added as sibling rule files.

Layout

config/config.yaml            workflow settings
annotations.tsv               samplesheet: annotations to QC (+ their genomes)
workflow/Snakefile            entry point
workflow/rules/*.smk          rules (extract_sequences, compleasm)
workflow/envs/*.yml           per-tool conda environments
workflow/scripts/             helper scripts
profiles/slurm/config.yaml    per-rule threads/resources
my_runner.sh                  SLURM submission script (Cannon)

Configuration

1. annotations.tsv — one row per annotation, tab-separated:

   column	meaning
   annotation_id	short unique label (used in output)
   annotation_path	path to the gff3 or gtf annotation
   genome_path	genome FASTA the annotation was built on

   Protein-level BUSCO requires CDS features in the annotation.

2. config/config.yaml

   • busco_lineage — BUSCO clade name, e.g. tetrapoda (see compleasm list --remote)
   • compleasm_odb — OrthoDB release (compleasm 0.2.8 default: odb12)
   • extract_tool — gffread (default) or agat
   • busco_downloads_dir — where the lineage database is stored/reused

Running (Cannon)

Requires a global cannon Snakemake profile in $HOME/.config/snakemake/cannon/ and a conda environment containing Snakemake (referenced in my_runner.sh).

sbatch my_runner.sh

Output

results/qc/busco_completeness.tsv — one row per annotation_id × level:

annotation_id  level  lineage  N_total  S  D  F  I  M  complete_frac  missing_frac  busco_score