Workflow use without Kneaddata

Infrastructure and utilities bioBakery workflows
1

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

2

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

Thank you,
Lauren

3

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

4

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

Thank you,
Lauren