The bioBakery help forum

Workflow use without Kneaddata

Hi, I wanted to know if there is an option where we can use the workflow on samples which already have been trimmed and filtered using kneaddata?
I want to use the orphan reads which are output from kneaddata and thus wish to know if I can bypass kneaddata and start directly from metaphlan using the cat file formed from paired1.fq, paired2.fq, unmatched1.fq, unmatched2.fq generated from Kneaddata.

Thanks in advance
DP

Hi DP, Yes you can. Just run the workflow with the option “–bypass-quality-control”.

Thank you,
Lauren

Hi lauren, thank you. Are these options listed anywhere (I couldn’t find them in the manual or the tutorial either).
Best
DP

Hi DP, If you run the tool with the --help option it will list all of the available options.

Thank you,
Lauren