using `alternatives` for aligners and assemblers and promoting common interfaces
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
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