---

Long-read Assembly

Workshop schedule

Lesson overview

• Introduction to the workshop
• How are assemblies created?
• Familiarize Ourselves with the Data
• Assembly
• Assembly QC
• Assembly clean-up
• Phased assemblies in action

Supplementary materials

Supplementary	Topic
Supplementary 1	NeSI HPC Authentication Factor Setup and Jupyter Login
Supplementary 2	NeSI File System, Working Directory, and Symlinks
Supplementary 3	Jupyter Virtual Desktop

Attribution notice

• Material used to prepare for the workshop was extracted from https://github.com/human-pangenomics/hprc-tutorials/tree/GA-workshop

References

• Lorig-Roach, Ryan, et al. "Phased nanopore assembly with Shasta and modular graph phasing with GFAse." bioRxiv (2023): 2023-02.

• Porubsky, David, et al. "Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads." Nature biotechnology 39.3 (2021): 302-308.

• Garg, Shilpa. "Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics." Nature Communications 14.1 (2023): 1358.

• Rautiainen, Mikko, et al. "Telomere-to-telomere assembly of diploid chromosomes with Verkko." Nature Biotechnology (2023): 1-9.

• Rhie, Arang, et al. "Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies." Genome biology 21.1 (2020): 1-27.