aviary isolate¶
Step-down hybrid assembly for isolated pure culture sequencing results. For use with isolate (not metagenomic) sequencing data.
This subcommand also accepts the common workflow, resource, output and execution options described under Shared options.
Examples¶
Long-read only¶
The minimum viable input — Flye assembly, racon and medaka polishing, then dnaapler reorientation. No illumina polishing round runs, since no short reads are given:
Hybrid: long reads + short reads for polishing¶
The typical case for a bacterial isolate closed with ONT and cleaned up with Illumina — adds one extra Pilon/racon polishing round using the short reads on top of the long-read assembly:
Short reads accept the same input shapes as the other subcommands:
aviary isolate -i sample_interleaved.fq.gz --longreads reads.fastq.gz --long-read-type ont
aviary isolate -c sample_1.fq.gz sample_2.fq.gz --longreads reads.fastq.gz --long-read-type ont
aviary isolate has no --long-read-assembler/--use-megahit/--use-unicycler flags — unlike
assemble/recover/complete, the isolate assembly path is fixed to Flye rather than
user-selectable, since it targets a single pure-culture genome rather than a mixed community.
Sizing the assembly¶
--genome-size is present in the CLI but is not currently consumed by the
workflow, so changing it does not alter the assembly. The following is accepted
for compatibility but behaves like the default invocation:
Input options (short reads)¶
Long reads (below) are required — isolate assembly is Flye-based and has no short-read-only path. Short reads are optional and, when given, are used for one additional Pilon/racon polishing round on top of the long-read assembly.
-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.
Input options (long reads)¶
-l, --longreads FILE [FILE ...]
Long-read files.
-z, --longread-type TYPE
Sequencing platform: rs, sq, ccs, hifi, ont, ont_hq. [default: ont]
--medaka-model MODEL
Model passed to the shared polishing helper. [default: r941_min_hac_g507]
Reads supplied above are mapped back onto the assembly for coverage and polishing. See Read mappers for the
--short-read-mapper/--long-read-mapperfamily of flags that control which aligner is used.
Isolate options¶
--guppy-model MODEL
Medaka model used by the isolate-specific polish_isolate_medaka rule.
Despite the historical option name, this is a Medaka model identifier.
The default is passed as a scalar; the current parser stores an explicit
override as a one-item list, so custom values should be treated as a known
compatibility limitation. [default: r941_min_hac_g507]
--genome-size INT
Accepted by the current CLI for compatibility, but not read by the current isolate workflow and therefore does not tune Flye. [default: 5000000]
QC options¶
Short-read and long-read filtering uses the same controls as assemble:
--host-filter, --gold-standard-assembly, --gsa-mappings,
--min-read-size, --min-mean-q, --keep-percent,
--min-short-read-length, --max-short-read-length,
--disable-adapter-trimming, --unqualified-percent-limit,
--quality-cutoff, --extra-fastp-params and --skip-qc. See
aviary assemble → QC options for types, defaults
and examples.
Performance 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
Accepted through the shared parser but not used by the default isolate workflow. [default: 8]
Output options¶
-o, --output DIR
Output directory. [default: ./]
--tmpdir DIR
Temporary files directory.
Inherited compatibility options¶
isolate also inherits the binning and database-path groups used by the
metagenome workflows. The default dnaapler isolate target does not use them:
--min-contig-size,--min-bin-size,--coverage-job-strategy,--coverage-samples-per-job,--semibin-model,--semibin-mode,--refinery-max-iterations,--refinery-max-retries,--extra-binners,--skip-binners,--binning-only,--skip-abundances,--skip-taxonomy,--skip-singlem,--min-completenessand--max-contamination--min-percent-read-identity-short,--min-percent-read-identity-long--gtdb-path,--eggnog-db-path,--singlem-metapackage-path,--checkm2-db-path,--metabuli-db-path
See aviary recover for the binning values and
aviary annotate for database
paths.