Genomic analyses using BLUPF90

SLU - Uppsala, Sweden

02 - 06 September 2019

Five-day course in genomic analyses with emphasis on single-step GBLUP

Taught by Ignacy Misztal and Daniela Lourenco (University of Georgia, USA)

BLUPF90 programs BLUPF90 Download

QMSim genomic data simulator QMSim Download

Xming Xming X Window System Server - for Windows

XQuatz X Quartz - for Mac

Putty 64-bit: putty.exe (the SSH and Telnet client itself)

MobaXterm Enhanced terminal for Windows with X11 server, tabbed SSH client, network tools and more

WinSCP WinSCP File Transfer

Editor Notepad++ Notepad++ 64-bit Installer

Course Outline

BLUPF90 Manual

Introduction to BLUPF90 suite programs

Day 1

• Introduction to blupf90 family

• Lab1

• Files for Lab1

• Script for lab1

Day2

• Genomic data

• Introduction to QMSim - simulating datasets

• Introduction to Linux commands - data manipulation

• Lab2

• Script for Lab2

• Script to edit data

Day3

• Quality control of genomic data in preGSf90

• Constructing genomic relationship matrix (G) in preGSf90

• General details about single-step GBLUP

Day4

• Seminar by Ignacy Misztal

• Script for Lab3_4

• Lab3_4

Day5

• SNP effects and GWAS with ssGBLUP

• Lab5

• Script for Lab5

• Lourenco et al., 2019a

• Legarra et al., 2018

• Misztal et al., 2017