"No samples found with any adapter contamination > 0.1%" Is adapter-trimming still necessary?

Question

[Jay-Run]

Hello, everyone,

After running fastqc on my raw data, I realized that the adapters are already removed (>%0.1). Would adapter-trimming in this case still improve the sequence quality? Or I can just skip it and only apply the quality-trimming?

Thank you. :)

Answer 1

[GenoMax]

Most aligners will soft-clip sequences that don't match a reference (e.g. adapters) so it is ok to omit scanning/trimming as long as you have a good reference to align to. If you are doing any de novo assembly work then you should scan/trim your sequences, no matter what FastQC says, to make sure all extraneous sequence bases are removed prior to assembly.