aviary assemble¶
Step-down hybrid assembly using long and short reads, or assembly using only short or long reads.
This subcommand also accepts the common workflow, resource, output and execution options described under Shared options.
Examples¶
Short-read only¶
Paired forward/reverse files (-1/-2) — the most common input shape:
Interleaved reads (-i), one file per sample with forward/reverse records alternating:
Coupled list (-c), forward and reverse files given as a single alternating list — an
alternative to -1/-2 for tools that already produce reads in this shape:
-1/-2, -i and -c are mutually exclusive: pick the one that matches how your reads are
laid out, not a combination.
By default, short-read-only assembly uses metaSPAdes. Swap to MEGAHIT (faster, lower memory, often the practical choice for very large or very deep datasets) or ask for a Unicycler re-assembly on top of the metaSPAdes result:
aviary assemble -1 reads_1.fq.gz -2 reads_2.fq.gz --use-megahit
aviary assemble -1 reads_1.fq.gz -2 reads_2.fq.gz --use-unicycler
Long-read only¶
Match --long-read-type to the actual chemistry — ont, ont_hq (Guppy5+/Q20 basecalling),
rs/sq/ccs (PacBio) or hifi (PacBio HiFi). This also selects the read-mapper preset used
for coverage calculation later, so an incorrect value affects more than just assembly.
Long-read assembly defaults to myloasm. Swap to Flye instead:
Hybrid (short + long reads)¶
Hybrid assembly uses the long reads to build a scaffold (via --long-read-assembler) and the
short reads to polish it; --use-megahit/--use-unicycler and --long-read-assembler both
still apply and combine freely with the flags above.
Multiple samples, coassembled¶
--coassemble is required (not just defaulted) whenever more than one read set is given —
aviary refuses to guess and exits with an error until you say explicitly whether to combine
them into one assembly or use only the first set for assembly (the rest are still used for
differential-coverage binning downstream):
aviary assemble -1 s1_1.fq.gz s2_1.fq.gz -2 s1_2.fq.gz s2_2.fq.gz --coassemble
aviary assemble -1 s1_1.fq.gz s2_1.fq.gz -2 s1_2.fq.gz s2_2.fq.gz --coassemble no
Input options (short reads)¶
-1, --pe-1 FILE [FILE ...]
Forward read files. If multiple files are provided and no longreads are given, all samples will be co-assembled with megahit or metaspades.
-2, --pe-2 FILE [FILE ...]
Reverse 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. The first file will be used for assembly unless --coassemble is set.
-z, --longread-type TYPE
Sequencing platform: rs (PacBio RSII), sq (PacBio Sequel), ccs (PacBio CCS), hifi (PacBio HiFi), ont (Oxford Nanopore), ont_hq (ONT high quality, Guppy5+ or Q20). [default: ont]
--long-read-assembler ASSEMBLER
Long-read assembler to use. myloasm (default) or flye. [default: myloasm]
--medaka-model MODEL
Medaka model for polishing long reads. [default: r941_min_hac_g507]
Reads supplied above are mapped back onto the assembly for coverage and racon polishing. See Read mappers for the
--short-read-mapper/--long-read-mapperfamily of flags that control which aligner is used.
Assembly options¶
--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. High long-read coverage indicates the overlap-layout-consensus assembly is more likely to be correct. [default: 5]
--min-cov-short INT
Automatically include Flye contigs with short-read coverage ≤ this value. Low short-read coverage indicates metaSPAdes would not assemble this contig better. [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".
Downstream compatibility options¶
Show details
The assemble parser also accepts the binning controls below because it shares
option groups with recover and complete. They do not affect the default
complete_assembly_with_qc target. They only become relevant if --workflow
is used to request a downstream binning rule:
--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-completeness,--max-contamination--min-percent-read-identity-short,--min-percent-read-identity-long
Their types, choices and defaults are documented under
aviary recover → Binning options.
Performance options¶
Show all 5 options
-t, --max-threads INT
Maximum threads given to any particular process. [default: 8]
-n, --n-cores INT
Maximum cores available. Setting to multiples of --max-threads allows parallel processes. [default: 16]
-m, --max-memory INT
Maximum memory in gigabytes. [default: 250]
-p, --pplacer-threads INT
Threads given to pplacer. [default: 8]
--local-cores INT
Maximum local cores when submitting to a cluster. [default: 16]
Output options¶
Show all 2 options
-o, --output DIR
Output directory. [default: ./]
--tmpdir DIR
Temporary files directory. Uses TMPDIR environment variable if not set.
Misc options¶
Show all 5 options
--snakemake-profile PROFILE
Snakemake profile for cluster submission. See the Guides section for HPC usage.
--cluster-retries INT
Number of retries for failed cluster jobs. [default: 0]
--dry-run
Perform a snakemake dry run.
--clean
Clean up temporary files after completion. [default: true]
--snakemake-cmds STRING
Additional snakemake commands as a single string.