Genomics Aotearoa Training: Long-Read Genome Assembly

This is an intermediate workshop, please check you meet the Prerequisites: Attendees must have introductory knowledge of Bash. We expect that you will either have completed our Introduction to bash workshop or have sufficient experience of your own.

Some of the topics covered in the workshop are:

• Sequence data basics: HiFi and UltraLong read data specifics
• Quality Control (QC) of the data: cleaning, read length filtering. Overview of phasing.
• Assembly of a genome: Verkko and Hifiasm, comparison of the approaches.
• Assembly QC: biological and technical assessments of the three Cs (contiguity, correctness, completeness).
• Contiguity using gfastats
• Correctness using Merqury
• Completeness using asmgene
• Assembly cleanup and genome annotation: checks for contamination, genome annotation using Liftoff, MashMap, and Minimap2.
• Phased assemblies: the power of phased assemblies, with examples.

Setup
This is a fully online, hands-on workshop. This workshop material will be run on the NeSI High Performance Computing (HPC) platforms – there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.

The material for this workshop can be previewed here.
Participants must have their own laptops and plan to participate actively. You will require a working web browser.

Register for this workshop at Eventbrite.

If you have any questions about these workshops, including whether they are suitable for you, please contact tyler.mcinnes@otago.ac.nz.