PhD thesis of Shaun Jackman
Efficient Assembly of Large Genomes
DNA sequencing machines read the A, C, G, and T nucleotides that compose chromosomes, but they read only short snippets of DNA and make errors. Dr. Jackman developed tools to reconstruct the true genome sequence from imperfect DNA sequencing reads. He used these tools to assemble the western redcedar genome, which is four times larger than human.
Contents
- Front matter
- Chapter 1: Introduction
- Chapter 2: ABySS 2.0 https://doi.org/10.1101/gr.214346.116
- Chapter 3: Tigmint https://doi.org/10.1186/s12859-018-2425-6
- Chapter 4: UniqTag https://doi.org/10.1371/journal.pone.0128026
- Chapter 5: ORCA https://doi.org/10.1093/bioinformatics/btz278
- Chapter 6: White spruce organelles https://doi.org/10.1093/gbe/evv244
- Chapter 7: Sitka spruce mitochondrion https://doi.org/10.1093/gbe/evaa108
- Chapter 8: Western redcedar https://doi.org/10.1101/gr.276358.121
- Chapter 9: Conclusions
- Appendix A: ABySS 2.0: Supplemental Material