Are there any tools that automatically detect where to truncate forward and reverse reads for 16S (DADA2)?

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1

I'm about to run DADA2 via QIIME2 and noticing that it's very hands-on and not completely automated.

Are there any reliable tools that can indicate where I should trim my forward and reverse reads based on input fastq?

Here's the documentation for the module I am running: denoise-paired: Denoise and dereplicate paired-end sequences — QIIME 2 2022.2.0 documentation

2

Is it not advised to merge all the reads, run through something like FastQC, and then find the region where the 25th percentile is lower than 30?

3

Hi @jolespin, welcome to :qiime2:!

The closest thing I can think of is figaro. There is also this thread.