This repository collects all the commands and script used for the Sardinian barley de novo assembly and pangenome project. This work is part of the PhD project carried out by Lia Obinu.
For the genome assembly methods see https://github.com/LiaOb21/colora
Some of the scripts used here were developed for the A. thaliana reference-free pangenome project and are available at: https://github.com/LiaOb21/arabidopsis_pangenome
If you use the code and methods described in this repository, please cite our work:
Lia Obinu, Timothy Booth, Heleen De Weerd, Urmi Trivedi, Andrea Porceddu, Colora: a Snakemake workflow for complete chromosome-scale de novo genome assembly, Bioinformatics, Volume 41, Issue 5, May 2025, btaf175, https://doi.org/10.1093/bioinformatics/btaf175
Lia Obinu, Andrea Guarracino, Urmi Trivedi, Andrea Porceddu, The reference-free pangenome of Arabidopsis thaliana, bioRxiv 2025.06.25.661508; doi: https://doi.org/10.1101/2025.06.25.661508