![image](theme_figures/institution_logos.png)
Long-read Assembly¶
![image](theme_figures/double_helix_mirror.png)
Workshop schedule
Lesson overview
Supplementary material
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
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Lorig-Roach, Ryan, et al. "Phased nanopore assembly with Shasta and modular graph phasing with GFAse." bioRxiv (2023): 2023-02.
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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.
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Garg, Shilpa. "Towards routine chromosome-scale haplotype-resolved reconstruction in cancer genomics." Nature Communications 14.1 (2023): 1358.
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Rautiainen, Mikko, et al. "Telomere-to-telomere assembly of diploid chromosomes with Verkko." Nature Biotechnology (2023): 1-9.
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Rhie, Arang, et al. "Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies." Genome biology 21.1 (2020): 1-27.