Worked analyses¶

These examples show how Aviary stages connect. Replace the illustrative paths with real input files; no example dataset is bundled with the repository.

Hybrid metagenome from reads to MAGs¶

Input¶

reads/
├── sample_R1.fastq.gz
├── sample_R2.fastq.gz
└── sample_ont.fastq.gz

Preview¶

aviary complete \
  -1 reads/sample_R1.fastq.gz \
  -2 reads/sample_R2.fastq.gz \
  --longreads reads/sample_ont.fastq.gz \
  --long-read-type ont \
  --output hybrid_complete \
  --max-threads 16 \
  --n-cores 32 \
  --dry-run

Run¶

Remove --dry-run after checking the planned targets and database paths:

aviary complete \
  -1 reads/sample_R1.fastq.gz \
  -2 reads/sample_R2.fastq.gz \
  --longreads reads/sample_ont.fastq.gz \
  --long-read-type ont \
  --output hybrid_complete \
  --max-threads 16 \
  --n-cores 32 \
  --max-memory 250

Interpret¶

Inspect assembly/final_contigs.fasta for the final assembly, bins/bin_info.tsv for the MAG summary and bins/final_bins/ for genome FASTA files. Check logs/ for rule execution details and benchmarks/ before adjusting scheduler requests.

Separate assembly and recovery¶

Splitting stages is useful when you want to inspect the assembly before committing to genome recovery.

aviary assemble \
  -1 reads/sample_R1.fastq.gz \
  -2 reads/sample_R2.fastq.gz \
  --output 01_assembly \
  --max-threads 16 \
  --n-cores 16

aviary recover \
  --assembly 01_assembly/assembly/final_contigs.fasta \
  -1 reads/sample_R1.fastq.gz \
  -2 reads/sample_R2.fastq.gz \
  --output 02_recovery \
  --max-threads 16 \
  --n-cores 32

The reads are supplied again because coverage across the assembly contributes to genome recovery and abundance estimation.

Annotate an existing genome collection¶

aviary annotate \
  --genome-fasta-directory 02_recovery/bins/final_bins \
  --fasta-extension fna \
  --output 03_annotation \
  --max-threads 16 \
  --n-cores 16

Keep the annotation run with the reference database releases used. See the annotation guide for interpretation and the CLI reference for advanced controls.