Potentially use Trimmomatic instead of trim_galore

[pvphaneuf]

According to https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4103590/, Trimmomatic give best alignment after adapter and quality trimming. Trimmomatic differs from trim_galore(Cutadapt) in that it uses a sliding window quality trimmer, which generally give better results than other quality trimming approaches.

Questions that need to be answered before substituting trimming software, where trim_galore currently accomplishes these tasks:

• [ ] Does Trimmomatic automatically detect adapter sequences?

[pvphaneuf]

Trimmomatic does not use adapter sequences. It is therefore difficult to incorporate into pipeline unless we've been given adapter sequences

[pvphaneuf]

Actually, it seems that Illumina does publish their adapter sequences: https://support.illumina.com/bulletins/2016/12/what-sequences-do-i-use-for-adapter-trimming.html