Genotyping by sequencing tutorial

authors: Cassandra Elphinstone and Yue Yu
level: Beginner
title: GBS tutorial
date: Jan 2025

Background

This is a tutorial to walk you through how to analyze GBS data. We will cover logging into the Digital Research Alliance servers, demultiplexing, references, mapping, SNP calling and plotting your data.

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Programs used in this tutorial

Below are a list of programs that we will use in this tutorial.

Perl

Perl scripts will be used to demultiplex the data

FastQC

Quality check your data

dDocent

dDocent is a pipeline that will walk us through building a de novo reference, mapping our reads to that reference and calling SNPs off that reference. It uses Rainbow to build the reference, and FreeBayes or GATK for SNP calling.

Admixture

Admixture is a program to look at population structure. It is a good way to tell if your data has been demultiplexed correctly.

R

R is a programming language that we will use to run a principal component analysis and plot our data. Libraries needed include: ggplot2,

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Useful Links

• Population genomics analyses: https://github.com/celphin/Population_genomics_Cassiope

• Genomic analysis: https://www.zoology.ubc.ca/~schluter/R/Genomics.html#SNP-calling_pipeline

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Zoom Recordings of past workshops

Jan 30th recording - Part 1:

Jan 31st recording - Part 2.1: Password: G?n$@=9Q

Jan 31st recording - Part 2.2: Password:*7.yVqU4