mykrobe_gene_deletion

[arnoldbain]

I have few MTB genomes that have deletions spanning resistance conferring genes such as katG, pncA etc but mykrobe predicts them as susceptible. Some of the deletions as big as 32kb. Can mykrobe handle such deletions in case one tries to create custom probes for such cases? Any idea of the size of the largest deletions/insertions that mykrobe can handle? Am using mykrobev0.12.1, thanks

[iqbal-lab]

Mykrobe is set up so you can add resistance genes to the panel - there are various genes that cause resistance in staph. It should not be hard to modify it to do the reverse also - call Resistance if a gene is absent. However it doesn't support that out of the box yet. We've been meaning to add this feature, especially for katG deletions, and to handle mmpL5 and mmpS5 for bedaquiline. No real length limit