Using trimmomatic before qiime2

[Nicholas_Bokulich]

I would recommend using q2-cutadapt to trim off adapters/primers instead of trimmomatic:

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

NOTE This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available in the q2-cutadapt plugin available in QIIME 2 2018.2. Please stay tuned here for additional updates as this tutorial is expanded upon in the coming weeks. Multiplexed reads with the barcodes in the sequence reads can be demultiplexed in QIIME 2 using the q2-cutadapt plugin, w…

The advantage is that this is all in QIIME 2, so the steps get stored in the provenance tracking, and you are much less likely to run into formatting issues.

In theory, using trimmomatic should be fine, but we have had some users report issues after attempting to import those data into QIIME 2. So go for it, but search the archive on this forum for "trimmomatic" to see other formatting troubleshooting that others have needed to do in the past.

Good luck!