To perform hybrid assembly:
aviary assemble -1 *.1.fq.gz -2 *.2.fq.gz --longreads *.nanopore.fastq.gz --long_read_type ont -t 24 -n 48
Aviary is compatible with both Nanopore and PacBio long read technologies. Note: Aviary can also perform assembly using just short or long reads as well.
aviary assemble -1 *.1.fq.gz -2 *.2.fq.gz -t 24 -n 48
OR
aviary assemble --longreads *.nanopore.fastq.gz --long_read_type ont -t 24 -n 48
To perform mag recovery:
aviary recover --assembly scaffolds.fasta -1 sr1.1.fq sr2.1.fq.gz -2 sr1.2.fq sr2.2.fq.gz --longreads nanopore.fastq.gz -z ont --output output_dir/ --max_threads 12 --n_cores 24 --gtdb_path /path/to/gtdb/release/
If no assembly file is provided, then aviary will first perform the assembly pipeline to produce an assembly using the input reads.
If at any point the Aviary workflow is interrupted, the pipeline can be restarted and pick up from the last completed step.
Often users are required to send long running jobs off on to high performance clusters. Aviary and snakemake are
perfectly compatible with clusters and can be sent off as either a single pipeline via PBS script or equivalent.
Alternatively, snakemake can send individual jobs in a pipeline off into a cluster to share the load across nodes.
You can make use of this feature in Aviary via the --snakemake-cmds
parameter, E.g.
aviary assemble -1 *.1.fq.gz -2 *.2.fq.gz --longreads *.nanopore.fastq.gz --long_read_type ont -t 24 -p 24 -n 24 --snakemake-cmds '--cluster qsub '
NOTE: The space after --cluster qsub
is required due to a strange quirk in how python's argparse
module works.
Aviary has three thread contol options:
-t, --threads
-n, --n-cores, --n_cores
--threads
, then potentially
multiple programs will run concurrently providing a great boost in performance. If this value is not set then it defaults
to being the same value as --threads
-p, --pplacer-threads, --pplacer_threads
When performing assembly, users are required to estimate how much RAM they will need to use via -m, --max-memory, --max_memory
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