Processing multiple files


I was wondering if there’s an easy way of using kneaddata for multiple files. Something along the lines of:

–input1 data/(xx)_R1_001.fastq.gz --input2 data/(xx)_R2_001.fastq.gz

So that it runs through everything in a particular folder?

Thank you!

Hello, You can use Kneaddata as part of the biobakery workflows. The workflows allow for batch processing of multiple samples through quality control (Kneadata), taxonomic profiling (MetaPhlAn), and functional profiling (HUMAnN) tools plus strain profiling (StrainPhlAn).


Hi Lauren,

Thank you for that.

I was just interested in using kneaddata in particular, rather than a workflow. Just wondering if there’s anything for that specifically?


Hi, Yes, you can run the workflow bypassing the steps that you do not want which should allow you to just run Kneaddata. Add the options --bypass-taxonomic-profiling --bypass-functional-profiling --bypass-strain-profiling to just run quality control processing with Kneaddata.

Thank you,