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Old 08-13-2014, 06:24 AM   #1
Location: Ha Noi

Join Date: Dec 2013
Posts: 29
Default cutadapt quality trimming cutoff algorithm

Hi all,
I 've use cutadapt to pre-processing my data but i have 2 quenstion about algorithm of quality trimminh in cutadapt:

1)Will Cutadapt scan from 3' end of read?
2)If scan from 3' end, is quality threshold (eg: 20) count by average quality or from which algorithm

Thanks in advance.
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Old 08-13-2014, 08:36 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

I posted a graph here comparing various quality trimming algorithms. Cutadapt was better than fastx and prinseq but outperformed by sickle, seqtk, and BBTools (the latter two use the Phred algorithm).

I'm not sure exactly what algorithm cutadapt is using, but it appears to perform better than simply stopping at the first base above a threshold.
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