MEGAHIT is an assembler that's optimized for metagenomes. For more information, see the tool's GitHub repo and wiki.

Function Call

toolchest.megahit(
    read_one=None,
    read_two=None,
    interleaved=None,
    single_end=None,
    output_path=None,
    tool_args="",
    is_async=False,
)
toolchest$megahit(
    read_one = NULL,
    read_two = NULL,
    interleaved = NULL,
    single_end = NULL,
    output_path = NULL,
    tool_args = "",
    is_async = FALSE
)

Function Arguments

See the Notes section below for more details.

ArgumentUse 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 Inputs and Outputs.
read_two-2(optional) Path to R2 of paired-end short read input files. The file can be a local or remote, see Inputs and Outputs.
interleaved--12(optional) Path to the file containing interleaved reads. The file can be a local or remote, see Inputs and Outputs.
single_end-r(optional) Path to the file containing singled-ended reads. The file can be a local or remote, see Inputs and Outputs.
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 Inputs and Outputs.
tool_argsall other arguments(optional) A string containing additional arguments to be passed to MEGAHIT, formatted as if using the command line.
is_asyncWhether to run a job asynchronously. See Asynchronous Runs for more.

Notes

Paired-end reads

For each paired-end input, make sure the corresponding read is in the same position in the input list. For example, two pairs of paired-end files – one_R1.fastq, one_R2.fastq, two_R1.fastq, two_R2.fastq – should be passed to Toolchest as:

tc.megahit(
  read_one=["one_R1.fastq", "two_R1.fastq"],
  read_two=["one_R2.fastq", "two_R2.fastq"],
  ...
)

Tool Versions

Toolchest currently supports version 1.2.9 of MEGAHIT.

Supported Additional Arguments

  • --min-count
  • --k-list
  • --k-min
  • --k-max
  • --k-step
  • --no-mercy
  • --bubble-level
  • --merge-level
  • --prune-level
  • --prune-depth
  • --disconnect-ratio
  • --low-local-ratio
  • --max-tip-len
  • --cleaning-rounds
  • --no-local
  • --kmin-1pass
  • --presets
  • --min-contig-len

Set additional arguments with tool_args. For example: tool_args="--no-local --no-mercy"


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