input files for Nonpareil 3

[INFINITY1993]

Hello,
Thanks for developing such an excellent tool.
For paired-end reads, how should I make the input file for Nonpareil 3? taking merged file of paired-end reads as input? or taking one of the paired-end files is also ok?
Best regards!

[jianshu93]

@lmrodriguezr Hello Miguel, I think we should add a description that Nonpareil/3 only supports forward or reverse reads at a time and results are very close. I find this question has been asked several times even though you made it clear in the documentation page but not the GitHub page. Most people will not be very careful about that detail in the documentation, can we make it more explicit.

Thanks,

Jianshu

[INFINITY1993]

Hello, Jianshu, thanks for the comments. I noticed that "Nonpareil should be applied on single reads, one of the sister
reads in paired-end reads, or merged paired-end reads", but I'm not sure I exactly understand the words. Thus, I posted the question. Thanks for your clear answer "Nonpareil/3 only supports forward or reverse reads at a time and results are very close".