Is there a benefict of denoising reads for project that are not using 16S amplicon ?

Question

[sacha]

Hi,

I just discovered "denoising" method in 16S amplicon analysis (DADA2, Deblur) . If I understood, this method can infer reads sequences without errors comming from technical process . ( an error model is computed ).

I wonder why we don't use this method for all projects which involved amplicon sequencing. For exemple, Can denoising help to be more accurate in cancer diagnosis when we need to detect a low frequency mutation which can be confused with an error ?

Answer 1

[Asaf]

The cases are different since with 16S you have a lot of different sequences in the amplicon and in the cancer variation example you have the main allele and variants which are a few or one so the case is much simpler. It can be used though for other amplicons that involve a lot of potential sequences as you mentioned.