nanopore sequencing - fastp dedup option

Question

[HarperReed]

Hello everyone, Should I use the dedup option when filtering my reads using Fastp while working on FASTQ files generated with Nanopore sequencing technology?

-D, --dedup enable deduplication to drop the duplicated reads/pairs

thank you in advance

[GenoMax]

Do you expect there to be sequence duplication because of the type of data (are these amplicon reads)? Depending on the length of your reads this could need significant memory/compute resources. Finally, what is the reason to want to do this?

[HarperReed]

it's amplicon sequencing of 1.5 to 3 kb. The primary aim is to detect variants.

[GenoMax]

You may want to try a workflow for this purpose provided by Nanopore: https://github.com/epi2me-labs/wf-amplicon

[HarperReed]

thank you !

[HarperReed]

But in my case, should I use this option or not? I don't really have time to test this new tool, especially since I'm required to use specific tools.

[GenoMax]

I'm required to use specific tools

If tools you are planning to use include a step to mark duplicates after alignments then you don't need to do this upfront.

Like I said above, depending on length of your amplicons (and amount of data) fastp may need compute resources to do the deduplication. You could give it a try and see if it works with nanopore data.

BTW; there is a fastplong version meant for long read data, but it does not have the -D option implemented as of now (https://github.com/OpenGene/fastplong?tab=readme-ov-file#all-options ).