simulate_fastq: simulate_fastq

In USDA-ARS-GBRU/crossword: Breeding program similation sotware

simulate_fastq

Description

The function simulates illumina fastq files (a paired-end or single-end) using ART.

Usage

simulate_fastq(single_reads,input,read_len,fold,art_binary_location,genotypes)

Arguments

single_reads	Optional: it direct the function to use paired-end, default FALSE, or single-end, TRUE, reads simulation
genotypes	Optional: it should be a hapmap file. If supplied, the fastq files will be simulated from real_time genomes produced from input fasta and genotypes containing in this hapmap file
input	Required: a fasta file or a directory contains a group of fasta files to be simulated, in this case the fold will be devided by number of the files in such directory
read_len	Optional: estimated read length, default is 250
fold	Optional: estimated read length, default is 30x
art_binary_location	Optional: the location of ART binary softwar, , default is art version implemented with this R package, 2016.06.05

Examples

simulate_fastq(FALSE,"test/a1.fa",read_len=250,fold=1.32"~/Documents/apps/art_bin_GreatSmokyMountains")
simulate_fastq(FALSE,"test",read_len=250,fold=1.32,"~/Documents/apps/art_bin_GreatSmokyMountains")

USDA-ARS-GBRU/crossword documentation built on April 5, 2023, 7:29 p.m.