Q score filtering

[elcor...@gmail.com]

Hello folks, 

Whereas, the quality filtering step in step 2.2 of the Amplicon SOP v2 (qiime2 2022.11) is set at default, the flag to specify the score according to

https://docs.qiime2.org/2024.5/plugins/available/quality-filter/q-score

is given as:

 --p-min-quality INTEGER 

The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores. [default: 4]

Does anyone know whether this default of "4" is really a PHRED score of 4 (which would be quite a low bar for filtering) or is that integer used to represent a PHRED score? (i.e., 1 = 10, 2 = 20 etc.,)

Can't seem to find the answer,

Cory

[Andre Comeau]

Yes, the default 4 actually means the low PHRED score of 4. It is really just there to make sure very odd/bad sequences get filtered out before heading into the ASV-creation step. See discussions here about the effect/need of q-filtering in both Deblur and DADA2:

https://qiita.ucsd.edu/static/doc/html/processingdata/deblur_quality.html

https://forum.qiime2.org/t/why-do-the-dada2-default-setting-have-such-a-low-phred-score/10156/2

The short of it all is that the (very) minimal Q-score filtering is just done to avoid any major breaking of the algorithms and that Deblur+DADA2 take care of the "quality issue" internally to themselves (focusing on error rates) and hence very stringent Q-filtering is actually counterproductive to their methods of working.

	ANDRÉ M. COMEAU, PhD Manager • Integrated Microbiome Resource (IMR) T: 902.494.2684 | E: andre....@dal.ca	​Address for deliveries: Dept. of Pharmacology Tupper Med. Bldg., room 5D Dalhousie University 5850 College St. Halifax NS B3H 4R2
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Subject: [microbiome-helper] Q score filtering

 

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[Cory Bishop]

Okay, that makes alot more sense Andre, thanks for that.

Cory

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