Sequencing, assembling, and annotating genomes with PacBio HiFi data

Over two days, Paul Frandsen (Brigham Young University) will provide workshop participants with 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.

schedule Date & time
18 Feb 2025 9:30am - 19 Feb 2025 5:00pm
person Speaker
Paul Frandsen, Brigham Young University, Utah
next_week Event series
CBA Workshops

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Description

Workshop 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, and other researchers who are interested in using whole genome sequencing in their research. 

Participants will need to bring their own laptops with an ssh application installed (further details will be provided to registered participants prior to the workshop). Registrations close Monday 10 Feb.

Day 1: Tues 18 Feb

Morning:

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

Afternoon:

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

Day 2: Wed 19 Feb

Morning:

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

Afternoon:

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

A light lunch will be provided each day in the break between sessions. The nearby Little Pickle cafe is also available for drinks and meals. There is a kitchenette with fridge and microwave next to the workshop room if you would like to bring your own.

Information about parking on campus is available here.

 

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 February 2025. 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.

Paul will also be giving a seminar at ANU on Thursday 20 February: Threading links between the silk genotype and phenotype in caddisflies, nature’s underwater architects.

Location

Jan Anderson Seminar Room, ground floor RN Robertson Building, ANU

-35.2781223, 149.1172712