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lmrodriguezr / nonpareil

Estimate metagenomic coverage and sequence diversity
http://enve-omics.ce.gatech.edu/nonpareil/
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input files for Nonpareil 3 #54

Open INFINITY1993 opened 2 years ago

INFINITY1993 commented 2 years ago

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 commented 2 years ago

@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 commented 2 years ago

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".