About TRF in kneaddata

Dear Kneaddata developers,

I would like to know more details about the TRF option in Kneaddata: why is it necessary to use TRF? And is it suggested to run kneaddata with TRF? I tried to find out the answer by looking at the manuscript for kneaddata, but it says “TBA” on the github repo. Many thanks!

Best wishes,
Shen

Hi @auas,

Thank you for reaching out to the biobakery Lab.
You can find a bit more about TRF parameters in the Kneaddata Tutorials below:

I will add more details on the TRF in the User manual as well. Thank you for the suggestion.

Regards,
Sagun

Hi Sagun,

Thank you for the information! I check the updated Github page and still have one question left: Is it suggested to run the trf in kneaddata? In other work, which situation is necessary to run trf?

Best wishes,
Shen

I notice the wiki says the trf does not run by default, but I never had to specify --run-trf argument and I can always see it did run in my logs. Has it been switched on to default in later versions ? If so, you must believe it is more necessary than not. I would also like to know what warrants removing tandem repeats.

I am assuming the tandem repeats are being removed in the same manner trimmomatic works, i-e trimming the entire read from where it finds a hit ?