[Question] Train module issue

[llk578496]

Hello @endixk ,

Thank you for developing this amazing pipeline! Our team are currently working on the clinical outbreak investigation on one of the most challenging multidrug-resistant fungi - Candida auris.

We would like to build a specific marker gene set for Candida auris by using the train module base on all the Candida auris genomes available on NCBI with complete/chromosome assembly level.

We have already downloaded a total of 45 genomes and created a directory containing all these reference genomes. However, when we tried to use the train module, we found that there was one more required option: -i STR Directory containing marker sequences in FASTA format (should be able to build an MSA).

May we know what data should we provide for this option?

Thank you very much!

Best regards, Eddie