Unicycler

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

Function Call

toolchest.unicycler(
    read_one=None,
    read_two=None,
    long_reads=None,
    output_path=None,
    tool_args="",
    is_async=False,
)
toolchest$unicycler(
    read_one = NULL,
    read_two = NULL,
    long_reads = NULL,
    output_path = NULL,
    tool_args = "",
    is_async = FALSE
)

Function Arguments

See the Notes section below for more details.

Argument

Use in place of:

Description

read_one

-1

(optional) Path to read 1 of paired-end short read input files. This can be a local filepath or an AWS S3 URI.

read_two

-2

(optional) Path to read 2 of paired-end short read input files. This can be a local filepath or an AWS S3 URI.

long_reads

-l

(optional) Path to the file containing long reads. This can be a local filepath or an AWS S3 URI.

output_path

-o

(optional) Path to a local directory where the output files will be downloaded.
If omitted, skips download. The outputs can be downloaded manually.

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.

Return Value

This function call returns a Toolchest output object, which contains the run ID and locations of downloaded output files. See Output Objects for more details.

Notes

Amazon AWS S3 inputs

Publicly available files stored on AWS's S3 service can be passed in as inputs, using the file's S3 URI.

Async runs

Set the is_async parameter to true if you would like to run a Unicycler job asynchronously. See Async Runs for more information.

Specifying input types

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. Every request to run Unicycler with Toolchest will default to this version.

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.


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