I'd like to hear your opinion regarding optimal trimming tool for transcriptome-assembly (2x150bp Illumina NovaSeq).
I generally use either fastp or Trimmomatic. I like the easy of use & speed of fastp. Also, the way fastp removes adapters I intuitively find very appealing. But the majority of users seems to stick to Trimmomatic.
I also think that the selection of the tool itself is not so much what decides the quality of the trimming (and the downstream assembly), but the correct settings of the tool.
What is your take on this?
I've used both tools for trimming reads prior to transcriptome assembly. Both are good tools and should probably get the job done in a majority of situations. I prefer fastp, mostly because it saves me from having to run a separate FastQC step.