A Chromosome-level assembly of Thymus vulgaris
As part of my Master’s program at BiRC, I worked with Thomas Bataillon 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.
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/
Mediterranean thyme (T. vulgaris) Obtained from Herbari virtual del Mediterrani Occidental