Adapter trimming using fastp

Question

[Shin Taguchi]

Hi everyone.

I use Trimmomatic for adapter trimming, but plan to use fastp in the future.

Adapter trimming with Trimmomatic allows us to specify seed mismatches, palindrome clips threshold, simple clip threshold, minAdapterLength, as in the following example:

ILLUMINACLIP:./Trimmomatic-0.39/adapters/NexteraPE-PE.fa:2:30:10:2

How can I specify the same conditions with fastp?

If you have any commands or scripts, I would appreciate it if you could let me know.

[barslmn]

Since these tools trim using different approaches I don't think you can translate that command to fastp one to one. These approaches being quoting from the fastp paper:

fastp supports automatic adapter trimming for both single-end and paired-end Illumina data and uses different algorithms for each of these tasks. For single-end data, adapter sequences are detected by assembling the high-frequency read tails; for paired-end data, adapter sequences are detected by finding the overlap of each pair.

Given that Trimmomatic, Cutadapt and SOAPnuke are all based on adapter-sequence matching, ...

The fastp paper has benchmarks against Trimmomatic. I suggest you create a small test set and try out different parameters and see if they output your desired results. Here is a video demonstrating various fastp parameters.

[Shin Taguchi]

Thank you for your reply! Your advice is very helpful. I would like to try different parameters as you mentioned.