Feature request- multiple paired read file input

[rotifergirl]

Hi!

Thanks for developing this great tool.

I'm trying to use this for multiple individuals, and I have multiple forward and reverse reads for each type. For now, I see that the best way is to concatenate my read files so I have a single forward and reverse for each individual, but it would be great to be able to avoid writing so many big files as an intermediate step (I see this was what you proposed in Issue #90 . Would you consider adding this functionality in future versions?