SimGBS.jl

A simple method to simulate Genotyping-by-Sequencing (GBS) data.
Author kanji709
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January 2021

SimGBS: A Julia Package to Simulate Genotyping-by-Sequencing (GBS) Data

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Installation

SimGBS.jl is registered in the General registry. It can be installed using Pkg.add,

julia> import Pkg;Pkg.add("SimGBS")

or simply

julia> ] add SimGBS

Input

  • Reference genome of the target species in FASTA format (e.g., xxx.fasta.gz/xxx.fa.gz)

  • Flie stores a list of Illumina barcodes (e.g., GBS_Barcodes.txt)

  • (optional) Pedigree File (e.g.,small.ped)

Output

  • GBS fragments generated by virtual digestion (e.g.,rawGBStags.txt)

  • Selected GBS fragments after fragment size-selection (e.g.,GBStags.txt)

  • Haplotypes, SNP and QTL genotypes (e.g.,hap.txt, snpGeno.txt and qtlGeno.txt)

  • File contains basic information about simulated GBS experiment (e.g.,keyFile.txt)

  • File contains simulated GBS reads in FASTQ format (e.g.,xxxxx.fastq)

etc.

Overview

More info can be found in documentation.

Citation

Please cite the following if you use SimGBS.jl,

  • Hess, A. S., M. K. Hess, K. G. Dodds, J. C. Mcewan, S. M. Clarke, and S. J. Rowe. "A method to simulate low-depth genotyping-by-sequencing data for testing genomic analyses." Proc 11th World Congr Genet Appl to Livest Prod 385 (2018).

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