Trimmomatic for cleaning NGS reads

Trimming and cleaning are important first steps in any analysis involving Illumina short read data. I’m somewhat familiar with the experimental protocols and why trimming, clipping, and filtering need to be done, but honestly I haven’t invested too much effort in familiarizing myself with the details of various implementations. I’ve essentially just used an R script from a colleague thus far for all my NGS preprocessing needs.

This week I came across a link for the Trimmomatic tool, which seems to be a well-implemented and reliable tool. I’m interested in comparing the performance of Trimmomatic versus my R script. I’m assuming Trimmomatic will be much faster and produce results of at least the same quality (if not better), in which case I would be happy to scrap the R script for good!

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