AlleleProfileR.simulate: Simulate paired-end reads from fasta files

In abruyneel/AlleleProfileR: Genome editing strategy agnostic variant identification and profiling tool

Description

This function samples reads from one or more fasta file using wgsim. This external software needs to be installed manually and needs to be addressable from the terminal. No data is returned: fastq.gz files are generated and deposited in the input.folder directory.

Usage

AlleleProfileR.simulate(input.folder, input.file,
  params = "-e 0 -d 250 -N 50000 -1 150 -2 150 -r 0 -R 0 -X 0")

Arguments

input.folder	Path to input fasta file folder
input.file	Vector with one or more .fas file names
params	Parameters for wgsim, default is: -e 0 -d 250 -N 50000 -1 150 -2 150 -r 0 -R 0 -X 0

References

• https://github.com/lh3/wgsim

abruyneel/AlleleProfileR documentation built on June 12, 2020, 2:47 p.m.