Sequencing, assembling, and annotating genomes with PacBio HiFi data

Workshop dates TBC*

Aims: Participants will gain knowledge and hands-on experience in analysing PacBio HiFi sequencing data, running whole genome assemblies, evaluating the quality of their genome assemblies, and will be introduced to whole genome annotation.

Target audience: students, postdocs, faculty who are interested in using whole genome sequencing in their research. Target size: ~20 participants.

Resources required: workshop room, personal computers with an ssh application and an internet connection

Day 1

  • Lectures: Designing a sequencing experiment, PacBio HiFi sequencing technology, sequencing QC.
  • Computational lab exercise: whole genome assembly with PacBio data.


  • Lecture: Genome quality assessment.
  • Computational lab exercises: genome assembly quality assessment (contiguity, BUSCO), duplicate purging, contaminant filtering.

Day 2


  • Lecture: What is a genome annotation, what are we trying accomplish?
  • Computational exercise: running evidence guided ab initio genome annotation.


  • Lecture: Functional genome annotation, potential pitfalls of annotation approaches.
  • Computational exercise: homology based functional genome annotation.


About Paul

Paul Frandsen is interested in evolutionary genomics and phylogenetics. His most recent work has focused on the genomic basis of silk production in caddisflies and lepidopterans and the use of genetic techniques in biodiversity monitoring. He also has considerable expertise in genome sequencing, assembly, and annotation.

*Paul is visiting ANU in the second half of 2024. His visit is funded by the Centre for Biodiversity Analysis, hosted Rob Lanfear (ANU). Please get in touch with Rob if you would like to meet with Paul during his time in Canberra.