UpalabdhaD / genome-assembly-workshop-2023

Genome assembly, curation and validation - workshop 2023

This repository contains the course materials for the EBP-Nor Genome Assembly Workshop that was given at the Norwegian Biodiversity Genomics & Conference. The course if run on infrastructure provdided by Sigma2.

You can grab the slides here.

To set up password, go here: https://www.metacenter.no/user/reset/.

Genome assembly, curation and validation - Schedule

09:00-12:00 Assembly

• 09:00-09:30 Introduction to whole-genome assembly and introduction to the study system and infrastructure
• 09:30-11:55 Assembling the sawfly genome
  • GenomeScope2
  • Smudgeplot
  • HiFiAdapterFilt
  • hifiasm
  • YaHS
  • Coffee break 10:45-11:15 together Genetic Diversity Monitoring Workshop
• 12:25-12:30 Summary

12:30-13:30 Lunch together with Genetic Diversity Monitoring Workshop.

13:30-14:15 Validation

• 13:30-13:45 Introduction to assembly validation
• 13:45-14:10 Interpreting assembly validation results
  • gfastats
  • BUSCO
  • Merqury
• 14:10-14:15 Summary

14:15-16:00 Decontamination and manual curation

• 14:15-14:30 Introduction to decontamination and manual curation
• 14:30-15:50 Decontaminating and curating the sawfly genome
  • FCS-GX
  • The GRIT Rapid Curation suite
  • Working in PretextView
• 15:50-16:00 Summary