First complete analysis

aviary complete joins assembly, genome recovery and annotation into one Snakemake run. Use it when you want Aviary to carry raw reads through to a curated set of metagenome-assembled genomes (MAGs).

Data flow

paired short reads ─┐
                    ├─ quality control ─ assembly ─ read mapping
optional long reads ┘                         │
                                              ▼
                         binning ─ refinement ─ quality assessment
                                              │
                                              ▼
                               taxonomy and functional annotation

Aviary orchestrates these stages; specialised dependencies perform the underlying assembly, binning, quality assessment and annotation algorithms.

Choose the input mode

Data available	Required input	Typical use
Paired short reads	-1, -2	Short-read metagenome assembly and recovery
Long reads	--longreads, --long-read-type	Long-read assembly and recovery
Both	short- and long-read options	Hybrid assembly and recovery
Existing assembly	--assembly plus reads for coverage	Skip de novo assembly and recover MAGs

See the input reference for pairing rules and accepted long-read type identifiers.

Run in a dedicated output directory

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 sample_aviary \
  --max-threads 16 \
  --n-cores 32 \
  --max-memory 250

The default maximum memory value in the workflow configuration is 250 GB. Set the option to the actual hard limit available to the run; it is not a prediction of typical memory consumption.

Monitor and resume

Rule-specific messages are written beneath logs/, while Snakemake benchmark records are written beneath benchmarks/. Re-running the same command and output directory normally resumes from existing valid outputs. Do not delete .snakemake/ or intermediate files while diagnosing an interrupted run.

For scheduler submission, resource caps and retries, see HPC and cluster submission. For precise command options, see the complete CLI reference.