Open pvphaneuf opened 7 years ago
Trimmomatic does not use adapter sequences. It is therefore difficult to incorporate into pipeline unless we've been given adapter sequences
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
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: