Class 13 16

Class 13. Tuesday, October 11, Long Reads I (In person.)

• Slides: Long Reads
• Reading: Opportunities and challenges in long-read sequencing data analysis - Amarasinghe 2020
• Lab: Long Reads I - QC and Assembly
• Class & Lab Recording

Class 14. Thursday, October 13, Long Reads II (In person.)

• Slides: Reference Genomes
• Reading
  • Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm Cheng et al 2021
  • BUSCO: Assessing Genome Assembly and Annotation Completeness - Mathieu Seppey et al 2019
  • The Human Pangenome Project: a global resource to map genomic diversity - Wang et al. 2022
• Lab: Long Reads II - CONDA ; BUSCO, Dot Plots, SyRI
• Class Recording
• Lab Recording

Class 15. Tuesday, October 18, Long Reads III (In person.)

• Slides: Pangenomes
• Reading
  • Computational pan-genomics: status, promises and challenges - The Computational Pan-Genomics Consortium, 2018
  • Plant pan-genomes are the new reference - Bayer et al 2020
  • Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement - Khan et al 2020
• Lab: Long Reads III - Mapping, Structural Variants
• Class & Lab Recording

Class 16. Thursday, October 20, Long Reads IV (In person.)

• Slides
• Reading:
  • Inferring synteny between genome assemblies: a systematic evaluation - Liu et al 2018
  • A comparative genomics multitool for scientific discovery and conservation- Zoonomia Consortium 2020
• Software:
  • Orthofinder: OrthoFinder: phylogenetic orthology inference for comparative genomics - Emms and Kelly 2019
  • MCScanX: MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity - Wang et al 2012
  • GeneSpace: GENESPACE tracks regions of interest and gene copy number variation across multiple genomes - Lovell et al 2022
  • SyRI: SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies - Goel et al 2019
  • Plotsr: [plotsr: visualizing structural similarities and rearrangements between multiple genomes](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0] - Goel et al 2022
• Test 3 - Due midnight Nov 3
• Lab: Long Reads IV - Comparing other genomes with Syri and RIdeogram
• Class & Lab Recording
• Screen
  • Screen instructions - the FULL docs
  • Screen cheatsheet - one of many out there, more convenient for casual use