aviary complete¶
Performs all steps in the Aviary pipeline: Assembly → Binning → Refinement → Annotation.
This subcommand also accepts the common workflow, resource, output and execution options described under Shared options.
| Jump to | |
|---|---|
| Input options | Read files and assemblies |
| Assembly options | Assembler choice, k-mers, Flye contig filtering |
| QC options | Read filtering and quality thresholds |
| Binning options | Binner selection, SemiBin2 mode/model, refinement, quality cutoffs |
| Annotation / bin processing options | Local database paths |
| Performance options | Threads, cores, memory |
| Output options | Output and temp directories |
| Misc options | Cluster profile, dry run, GPU request |
| Examples | Common flag combinations |
Examples¶
The basic shape — assembly, binning and annotation in one call:
complete accepts every input shape and assembler flag documented in
aviary assemble (-1/-2, -i, -c, -l, --use-megahit,
--long-read-assembler) and every binning flag in aviary recover
(--semibin-model, --extra-binners, --min-completeness, etc.), since it runs both stages
back to back. The examples below are scenarios where combining flags across those two stages
in a single complete call is the actual point, rather than running each stage separately.
A realistic hybrid run, soil metagenome, time series¶
Long and short reads for three related samples, coassembled per-sample, SemiBin2 multi-sample binning to use cross-sample abundance, and a stricter completeness cutoff before annotation:
aviary complete \
-1 week1_1.fq.gz week2_1.fq.gz week3_1.fq.gz \
-2 week1_2.fq.gz week2_2.fq.gz week3_2.fq.gz \
--longreads week1.ont.fq.gz week2.ont.fq.gz week3.ont.fq.gz --long-read-type ont \
--semibin-mode multi --semibin-model soil \
--min-completeness 70 --max-contamination 5 \
-o soil_timeseries/ -t 16 -n 64
Fast turnaround on a preliminary assembly¶
Skip taxonomy and abundance to get bins quickly for a first look, without wiring up GTDB-tk or running CoverM abundance yet:
Or keep abundance but drop only the slowest annotation step:
Re-running from an assembly you already have¶
If you already assembled separately (e.g. to inspect it first, or because you built it with
another tool), complete skips straight to binning and annotation:
Multiple assemblies through the whole pipeline¶
SemiBin2 multi-sample binning also works when complete builds the assemblies itself, given
one read set per sample:
aviary complete --assembly sample1.fasta sample2.fasta \
-1 sample1_1.fq.gz sample2_1.fq.gz -2 sample1_2.fq.gz sample2_2.fq.gz \
--semibin-mode multi
Input options¶
-a, --assembly FILE [FILE ...]
One or more FASTA files containing scaffolded contigs of metagenome assemblies. If not provided, aviary will assemble first. Provide multiple assemblies for SemiBin2 multi-sample binning (requires --semibin-mode multi).
-1, --pe-1 FILE [FILE ...]
Forward short read files.
-2, --pe-2 FILE [FILE ...]
Reverse short read files.
-i, --interleaved FILE [FILE ...]
Interleaved read files.
-c, --coupled FILE [FILE ...]
Forward and reverse read files in a coupled space-separated list.
-l, --longreads FILE [FILE ...]
Long-read files.
-z, --longread-type TYPE
Sequencing platform: rs, sq, ccs, hifi, ont, ont_hq. [default: ont]
Reads supplied above are mapped back onto the assembly for coverage, abundance and polishing. See Read mappers for the
--short-read-mapper/--long-read-mapperfamily of flags that control which aligner is used.
Assembly options¶
--long-read-assembler ASSEMBLER
Long-read assembler: myloasm or flye. [default: myloasm]
--medaka-model MODEL
Medaka model for long-read polishing. [default: r941_min_hac_g507]
--use-unicycler
Use Unicycler to re-assemble the metaSPAdes hybrid assembly. Not recommended for complex metagenomes.
--use-megahit
Use MEGAHIT instead of metaSPAdes for short-read-only assembly. [default: false]
--coassemble, --co-assemble
When multiple read sets are given, coassemble them together. If false, aviary uses only the first short-read and first long-read set for assembly (all read sets are still used for differential-coverage binning). [default: false]
-k, --kmer-sizes INT [INT ...]
Manually specify the k-mer sizes used by SPAdes during assembly. Space-separated odd integers less than 128, or auto. [default: auto]
--min-cov-long INT
Automatically include Flye contigs with long-read coverage ≥ this value. [default: 5]
--min-cov-short INT
Automatically include Flye contigs with short-read coverage ≤ this value. [default: 5]
--exclude-contig-cov INT
Automatically exclude Flye contigs with long-read coverage ≤ this value, provided their length is also ≤ --exclude-contig-size. [default: 10]
--exclude-contig-size INT
Automatically exclude Flye contigs with length ≤ this value, provided their long-read coverage is also ≤ --exclude-contig-cov. [default: 2500]
--include-contig-size INT
Automatically include Flye contigs with length ≥ this value. [default: 10000]
QC options¶
Show all 13 options
-r, --host-filter FILE [FILE ...]
Host reference FASTA files for removal of contaminant reads prior to assembly.
-g, --gold-standard-assembly FILE [FILE ...]
A gold-standard assembly to compare the resulting (or a given input) assembly against.
--gsa-mappings FILE
CAMI I & II gold-standard-assembly mappings, used alongside --gold-standard-assembly.
--keep-percent INT
Deprecated
Percentage of reads passing quality thresholds kept by Filtlong. [default: 100]
--skip-qc
Skip quality control steps.
--min-read-size INT
Minimum long read size when filtering using Filtlong. [default: 100]
--min-mean-q INT
Minimum long read mean quality threshold. [default: 10]
--min-short-read-length INT
Minimum length of short reads to keep. [default: 15]
--max-short-read-length INT
Maximum length of short reads to keep, 0 = no maximum. [default: 0]
--disable-adapter-trimming
Disable adapter trimming of short reads.
--quality-cutoff INT
Phred quality value threshold for short reads. [default: 15]
--unqualified-percent-limit INT
Percentage of bases allowed to be unqualified. [default: 40]
--extra-fastp-params STRING
Extra parameters to pass to fastp, e.g. --extra-fastp-params "-V -e 10".
Binning options¶
-s, --min-contig-size INT
Minimum contig size in base pairs for binning. [default: 1500]
-b, --min-bin-size INT
Minimum bin size in base pairs for a MAG. [default: 200000]
--extra-binners BINNER [BINNER ...]
Extra binning algorithms to run: maxbin/maxbin2 (equivalent), concoct, comebin, taxvamb, quickbin. These are skipped by default due to long runtimes.
--skip-binners BINNER [BINNER ...]
Binning algorithms to skip: rosella, semibin, metabat1, metabat2, metabat and vamb.
--semibin-model MODEL
SemiBin2 environment model: human_gut, dog_gut, ocean, soil, cat_gut, human_oral, mouse_gut, pig_gut, built_environment, wastewater, global. [default: global]
--semibin-mode {single,multi}
SemiBin2 mode to use. single runs single_easy_bin on one assembly at a time. multi runs multi_easy_bin, co-binning multiple assemblies together — pass two or more files to --assembly to use it. Multi mode ignores --semibin-model, as pre-trained environments aren't supported for multi-sample binning. [default: single]
aviary complete --assembly sample1.fasta sample2.fasta sample3.fasta \
-1 sample1_1.fq.gz sample2_1.fq.gz sample3_1.fq.gz \
-2 sample1_2.fq.gz sample2_2.fq.gz sample3_2.fq.gz \
--semibin-mode multi
Assemblies are concatenated (with unique sample:contig headers) into one SemiBin2 input, and reads from every sample are mapped back onto that concatenation, so co-abundance across samples improves binning. Output bins are written per-sample-prefixed into data/semibin_bins/output_bins/.
--refinery-max-iterations INT
Maximum Rosella refinery iterations. Set to 0 to skip. [default: 5]
--refinery-max-retries INT
Maximum Rosella refinery retries per iteration. [default: 3]
--binning-only
Stop after binning. Skip SingleM, GTDB-tk, and CoverM.
--skip-abundances
Skip CoverM post-binning abundance calculations.
--skip-taxonomy
Skip GTDB-tk post-binning taxonomy assignment.
--skip-singlem
Skip SingleM post-binning recovery assessment. [default: true]
--min-completeness FLOAT
Minimum CheckM2 completeness percentage for bins retained in downstream processing. [default: 50.0]
--max-contamination FLOAT
Maximum CheckM2 contamination percentage for bins retained in downstream processing. [default: 5.0]
--coverage-job-strategy STRATEGY
Strategy for coverage calculation across many samples: default, never, always. [default: default]
--coverage-samples-per-job INT
Number of samples per coverage job when splitting. [default: 5]
--min-percent-read-identity-short FLOAT
Minimum percent read identity used by CoverM for short reads when calculating genome abundances. [default: 95]
--min-percent-read-identity-long FLOAT
Minimum percent read identity used by CoverM for long reads when calculating genome abundances. [default: 85]
Annotation / bin processing options¶
Show all 5 options
--gtdb-path PATH
Path to local GTDB database files.
--eggnog-db-path PATH
Path to local EggNOG database files.
--singlem-metapackage-path PATH
Path to local SingleM metapackage.
--checkm2-db-path PATH
Path to CheckM2 database.
--metabuli-db-path PATH
Path to local Metabuli database.
Performance options¶
Show all 5 options
-t, --max-threads INT
Maximum threads per process. [default: 8]
-n, --n-cores INT
Maximum cores available. [default: 16]
-m, --max-memory INT
Maximum memory in gigabytes. [default: 250]
-p, --pplacer-threads INT
Threads for pplacer. [default: 8]
--local-cores INT
Maximum cores available locally. Only relevant when submitting to a cluster (see --snakemake-profile), in which case --n-cores restricts cores requested per submitted job. [default: 16]
Output options¶
Show all 2 options
-o, --output DIR
Output directory. [default: ./]
--tmpdir DIR
Temporary files directory.
Misc options¶
Show all 7 options
--snakemake-profile PROFILE
Snakemake profile for cluster submission. See the Guides section for HPC usage.
--cluster-retries INT
Retries for failed cluster jobs. [default: 0]
--dry-run
Perform a snakemake dry run.
--clean
Clean up temporary files. [default: true]
--strict
Ensure each binner completes successfully. [default: skip failing binners]
--request-gpu
Request a GPU for the pipeline (taxvamb, comebin, semibin). Only takes effect when run on a cluster. [default: false]
--snakemake-cmds STRING
Additional commands passed through to snakemake as a single string, e.g. --snakemake-cmds "--print-compilation True". Most snakemake -h commands are valid, but some may clash with commands aviary supplies directly — check for conflicts before using.