Can I run Kneaddata with catenated forward and reverse reads file?

[DEEPCHANDA7]

Hi @franzosa !!! As much as I know, for MetaPhlAn 3.0 we can catenate the forward and reverse reads into a single file. We can run that single file with metaphlan command. Like that, can we also run this single file with kneaddata? I mean, should I run the forward and the reverse reads separately or I can run after concatenating them into a single file?

Thanks
DC7

[sagunmaharjann]

Hi @DEEPCHANDA7,

Please refer to the documentation on How to run paired-end sequence using Kneaddata.

Thanks,
Sagun