# rh04 / 63_rh04 GenoAdjust demo genome

This directory contains the public reproducibility input used by the
GenoAdjust Empty Quarter demo.

## Genome

- Sample: `rh04`
- Assembly / MAG identifier: `63_rh04`
- Organism assignment: `Bacillus spizizenii`
- NCBI Taxon ID: `96241`
- ANI status: `CONFIRMED`
- ANI confidence: `HIGH`
- Assembly size: 4,258,061 bytes

## Files

- `genome_63_rh04_assembly.fa.gz`: genome assembly FASTA.
- `pgap_annot.gff.gz`: PGAP GFF annotation used by the GenoAdjust demo.
- `pgap_annot.faa.gz`: PGAP protein FASTA.
- `pgap_annot.fna.gz`: PGAP nucleotide feature FASTA.
- `ani-tax-report.txt`: PGAP ANI taxonomy report.
- `checkm.txt`: CheckM quality summary.
- `manifest.json`: machine-readable provenance and file list.
- `SHA256SUMS`: SHA-256 checksums for the files in this directory.

## Source paths on IBEX

- `/ibex/scratch/projects/c2014/EmptyQuarter_Data/processed/sequencing-results/rh_sequencing/rh04/assembly/63_rh04_assembly.fa`
- `/ibex/scratch/projects/c2014/EmptyQuarter_Data/cultures/assemblies/assemblies_tiannyu_2025/pgap_annotations/63_rh04/`

The demo converts GO annotations from `pgap_annot.gff.gz` into the GenoAdjust
`GO|score` prediction format and uses `ani-tax-report.txt` only for reporting.