The following external software is run as part of pangolin:
Heng Li, Minimap2: pairwise alignment for nucleotide sequences, Bioinformatics, Volume 34, Issue 18, 15 September 2018, Pages 3094–3100, https://doi.org/10.1093/bioinformatics/bty191
Colquhoun & Jackson. 2021
Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.