Transcriptome assembly -- fastp vs Trimmomatic

Question

[Michael]

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?

[Dave Carlson]

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.

[tommy]

I am choosing fastp now due to the fact I am new to the area and puzzled with parameter settings in trimmomatic. Sometimes, unsuitable settings lead to truncated sequencings in the following steps.

Answer 1

[Istvan Albert]

The selection of trimming tool (as long as it is operates correctly) has very little effect on the quality of subsequent analysis.

Often we choose trimming tools based on:

1. performance of the tool - both correctness and efficiency
2. familiarity and convenience
3. needing a specific functionality that only a particular tool offers

Trimmomatic was one of the first tools that worked well, it is highly performant hence for many became the last tool trimming tool that many ever needed to try.

[Michael]

Istvan Albert Thanks much for your reply. So you agree that for a transcriptome assembly (given correct parametrization) fastp vs Trimmomatic is more a matter of taste ;)