run_megahit: This script is a R wrapper for the bash script megahit.sh to...

In uashogeschoolutrecht/structural_colours: Package For Project Structural Colour

Description

This script is a R wrapper for the bash script megahit.sh to run the megahit assembly tool

Usage

run_megahit(
  PE = T,
  nohup = "",
  script_path,
  r1,
  r2 = "",
  outdir,
  outname = "megahit"
)

Arguments

PE	TRUE/FALSE. Wether paired end or single end library is supplied. Default = T
nohup	can be set to "nohup" to run assembly in background. Default = ""
script_path	Path to megahit.sh, e.g. "/home/$USER/scpackage/inst/megahit.sh"
r1	Path to read file one, paired end or single end
r2	Path to paired end read
outdir	Existing directory to create output directory in
outname	Output directory name, will be created by program

Value

A directory with output files will be created at supplied path

Examples

run_megahit(script_path = "/home/$USER/scpackage/inst/megahit.sh",
r1 = "/home/$USER/data/geodescent/samples/MGYS00000991/ERR1424899_1.fastq.gz",
r2 = "/home/$USER/data/geodescent/samples/MGYS00000991/ERR1424899_2.fastq.gz",
outdir = "/home/$USER",
outname = "megahit_testing")

uashogeschoolutrecht/structural_colours documentation built on June 20, 2020, 4:07 p.m.