Hi, all, Another thought that has been floating around in my head: we have many read aligners, variant/consensus callers, genome assemblers, and other such tools that do the same job with different algorithms. I think it makes sense to try to manage them as alternatives[1] and work towards standardizing their interfaces.
I also think that the variation in interfaces for these similar tools is not because of any developer's attachment to them, but because there's no real guideline for what to do (like, how to pass the reference sequence-- some say -r while others might say --referenceFile). On the other hand, besides better organization and potentially more intuitive interfaces, I'm not sure whether undertaking this is worth the effort. Are there any strong feelings about this? regards Afif 1. https://wiki.debian.org/DebianAlternatives -- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name
