Unicycler is an assembly pipeline for bacterial genomes. For more information, see the tool's GitHub repo and wiki.

Function Call

tc.unicycler(
    read_one=None,
    read_two=None,
    long_reads=None,
    output_path=None,
    tool_args="",
    is_async=False,
)

Function Arguments

Argument	Use in place of:	Description
read_one	-1	(optional) Path to R1 of paired-end short read input files. The file can be a local or remote, see Using Files.
read_two	-2	(optional) Path to R2 of paired-end short read input files. The file can be a local or remote, see Using Files.
long_reads	-l	(optional) Path to the file containing long reads. The file can be a local or remote, see Using Files.
output_path	-o	(optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see Using Files.
tool_args	all other arguments	(optional) Additional arguments to be passed to Unicycler. This should be a string of arguments like the command line. See Supported Additional Arguments for more details.
is_async		Whether to run a job asynchronously. See Async Runs for more.

Notes

Paired-end reads

Paired-end short read inputs should be specified with both read_one and read_two.

Tool Versions

Toolchest currently supports version 0.4.9 of Unicycler.

Supported Additional Arguments

• --depth_filter
• --kmer_count
• --kmers
• --largest_component
• --linear_seqs
• --low_score
• --max_kmer_frac
• --min_component_size
• --min_dead_end_size
• --min_fasta_length
• --min_kmer_frac
• --min_polish_size
• --mode
• --no_correct
• --no_miniasm
• --no_pilon
• --no_rotate
• --scores
• --start_gene_cov
• --start_gene_id
• --verbosity

Additional arguments can be specified under the tool_args argument.