Long Read Adapter Trimming in Aviary?

[Anna-MarieSeelen]

Hi Aviary team,

I'm using Aviary 0.11.0 for a hybrid assembly of nanopore reads and short reads. I noticed that some adapter sequences from the raw nanopore reads are still present in the final_contigs.fasta file. I see that chopper is used to trim long reads, but it doesn’t seem to remove adapters — is that correct?

If there’s no adapter trimming for long reads in the pipeline, would you recommend trimming them before using aviary to do a hybrid assembly?

Thanks,

Anna