Primer/adapter trimming for antibody sequencing data?

Question

[aishwarya.n8]

I m looking at papers that go into detail about the primer design and adapters used during the library prep but no mention of trimming is made in the data processing description. Is trimming done as part of the data processing step? If yes, could someone please suggest the recommended softwares for this step?

Answer 1

[Brian Bushnell]

The current best adapter-trimming software is BBDuk. This is the recommended protocol. And yes, adapter-trimming is crucial as a preprocessing step of all Illumina data.