About TRF in kneaddata

Infrastructure and utilities KneadData
1

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

2

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

3

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

4

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 ?

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Is it recommended before co-/assembly ?

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Hello, I would just like to follow up on this, since I don’t think the main initial question has been answered. What is the reason for the TRF step in kneaddata and in which situations is it necessary to clear tandem repeats? I was not aware this should be done before seeing it in this pipeline…

1 Like
7

Any follow up?
Thanks!