(Optionally) show read counts to individual host sequences

[rzelle-lallemand]

We would like to use hostile to filter out reads matching certain reference sequences, but we're interested in knowing what number of reads align to each reference sequence, without having to run hostile multiple times against individual reference sequences. It would be great if hostile could optionally report this metric.

See https://www.biostars.org/p/14531/#14536 for related discussion.

[bede]

I agree that it would be nice to optionally include this information in the output log. I'll reply again once I've taken a look. Thanks

[bede]

Hi @rzelle-lallemand, Sorry for delay. I'm afraid that I am reluctant to add this feature to Hostile for complexity and performance reasons. I am however considering adding similar functionality to Deacon, a very fast search and depletion tool. If you're interested, please reach out to me using the email in my profile and we can discuss whether this would likely suit your use case.