Request: output all variants per gene

[sav-che]

Hi and thanks for the nice resource!
Am I right that align module always takes only one variant of multicopy genes? For the sake of, e.g., contamination search, it would be nice to have fasta for each gene (aligned or not) with all gene variants of all samples. Now it is possible to do only by rearranging profile or profile-convert outputs with some custom script. I have tried align -c 1, but it seems to do another thing.

[endixk]

Hello, thank you for your kind words!

You are correct; Currently our pipeline isn't capable of processing the variants, i.e. sub-optimal sequences detected by the profile module. align -c 1 allows the optimal copy among these multiple copies to be included in the subsequent analysis.

I do agree that it will be useful to develop a module that produces FASTA files of the detected core genes. I will try to implement this before the next release.

[sav-che]

Thanks. It is of course will not be suitable for concatenated tree, but will be surely useful for many other things.