suggestion: new input option for ska build (1 file containing n isolates)

[rderelle]

I’ve been playing a bit with SKA2 and a dataset of around 2400 mpox genomes to test k-mer sizes and SNP callers. It worked well overall, but I found it a bit tedious to have to create one input file per genome.

Do you think it would be possible/suitable to add an input option—on top of '-f'—that treats each sequence in a multi-sequence file as a separate isolate? It might be helpful for viral datasets.

[johnlees]

It's a good idea, I did this in sketchlib.rust with the --concat-fasta option.

Code here if you want a reference to give it a go https://github.com/bacpop/sketchlib.rust/blob/main/src/sketch.rs#L283-L329

[rderelle]

Ok thanks. I'll give it a try early next week.