Sliding windows and quality filtering

Hello Aaron,

Yes, there are a few programs that trim using a sliding window! See this thread on trimmomatic or maybe this fork of sickle.

In case you have not found these already, here's the DADA2 ITS pipeline workflow in R and the Qiime2 Fungal ITS tutorial.

It looks like they both use cutadapt to remove adapters instead of trimming by length or q-score. Interesting!