grinder: Runs the biogrinder program to create artificial fastq reads...

In uashogeschoolutrecht/structural_colours: Package For Project Structural Colour

Description

Runs the biogrinder program to create artificial fastq reads from input genomes.

Usage

grinder(
  reference_file,
  abundance_file = "",
  fastq_output = "1",
  qual_levels = "35 10",
  mutation_dist = "poly4 3e-3 3.3e-8",
  outname,
  outdir,
  coverage = "1"
)

Arguments

reference_file	Fasta file of genomes, path
abundance_file	File of bundances of each genome for the reads, per line of file "name 22" name and perc.
fastq_output	Default is 1, (true)
qual_levels	Two quality values will be given: good / bad, default: "35 10"
mutation_dist	Default is for Illumina sequences
outname	Prefix name of output files
outdir	Directory to store output files in
coverage	Library coverage

Examples

grinder(reference_file = "/home/$USER/scpackage/inst/extdata/GCA_002277835.1_ASM227783v1_genomic.fna",
abundance_file = "/home/$USER/abundance.txt",
outname = "test_grinder",
outdir = "grinder")

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