This semester, I worked with my supervisor Thomas Bataillon as part of my Master’s program at BiRC on a Bioinformatics project. Our goal was to use Pacbio HiFi reads to obtain a chromosome-level assembly of Mediterranean thyme.
The primary objective was to use the genome of a closely related species to improve the contiguity of the highly fragmented de novo assembly. Although further research is required, we achieved promising results. For example, we increased the N50 from 1.87 Mb (n=133) at the contig level to 48.92 Mb (n=8) at the scaffold level. An outline of the pipeline can be found here.
Working with plant genomes has been challenging, and I have learned a lot about genome assembly with long reads and plant genomes. Additionally, this project was part of a broader investigation into the genetic and ecological diversity of Mediterranean thyme, a subject that I found fascinating.
I utilized the GenomeDK cluster at the center for the data analysis pipeline, employing various programs and programming languages, including R, Python, Julia, and Bash.
All the code and the slides I used for the project defense are publicly available on GitHub, which you can access at https://currocam.github.io/BiRC-Thyme/