Long-read Assembly¶
Workshop schedule
| Day | Time | Lesson overview |
|---|---|---|
| Tuesday, 4th July | 1:00PM 2:00PM 3:00PM |
Introduction to the workshop How are assemblies created? Familiarize Ourselves with the Data Talk by Assistant Professor Karen Miga |
| Wednesday, 5th July | 9:00AM 12:00PM 1:00PM 2:00PM 3:00PM |
Assembly Lunch break Assembly continued Talk by Dr Brandon Pickett Talk by Dr Joseph Guhlin |
| Thursday, 6th July | 9:00AM 10:00AM 11:00AM 12:00PM 1:00PM |
Assembly QC Assembly clean-up Phased assemblies in action Lunch break Talk by Assistant Professor Benedict Paten |
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.