Course on Manual Genome Curation Using PretextView!
Dates: 11th - 15th November 2024
Location: Online (to foster international participation)
Course website: https://www.physalia-courses.org/courses-workshops/genome-curation/
COURSE OVERVIEW:
Dive into the world of manual genome curation with our comprehensive course on using PretextView. Learn the fundamental concepts of Hi-C sequencing and its significance in genome curation. From understanding assembly quality metrics to identifying sex chromosomes, we'll cover everything you need to deliver high-quality chromosome assemblies.
TARGET AUDIENCE & ASSUMED BACKGROUND:
Ideal for biologists and bioinformaticians, this course blends lectures and hands-on exercises. While prior experience with the Unix command-line is recommended, genome assembly expertise is not required.
LEARNING OUTCOMES:
- Understand how the assembly and Hi-C data quality are vital for efficient genome curation.
- Be able to interpret Hi-C heatmaps in PretextView and identify the edits necessary to fix assembly errors.
- Use PretextView and its features for manual curation.
- How to obtain a genome curated fasta file using the Rapid Curation pipeline.
- Become familiar with additional tools used to curate more challenging genomes (microchromosomes, high heterozygosity) and how to identify sex chromosomes.
PROGRAM:
Day 1: Manual curation overview and assembly quality metrics
Day 2: Hands-on decontamination and beginning manual curation
Day 3: Generating PretextView Hi-C maps and using PretextView
Day 4: Strategies for challenging genomes and sex chromosome identification
Day 5: Practical sessions on challenging genomes and group discussions
