Mike Weigand

I had a related issue. The README hints that genomic regions can be masked by passing a bed file to parameter '--mask'. However, this option is not listed in the...

@Pragungrb I determined that the '--mask' parameter was only applicable when running 'snippy-core' which probably makes sense because avoids potential downstream artefacts during core calculation if masking isn't consistent among...

@avonm did you figure this out? I can only get `--proteins` to work with an faa downloaded directly from NCBI but not one that I've curated myself.

Here's a specific example, output from assembly of Illumina NovaSeq reads from monkeypox virus. Note segment 12 has no sequence (length = 0 bp). ```console cat L*A13.assembly.gfa | grep ^S...