Program to demultiplex before to use DADA2

Question

[domingues.pesca]

Hello everyone!

I have metabarcoding sequences and would like to use DADA2 for my analysis, but I need to demultiplex the samples before it. Which program should I use to demultiplex samples bedofe to use DADA2 for metabarcoding downstream analysis? I really appreciate any help you can provide.

Answer 1

[hjarnek]

Use cutadapt. Very versatile and well-tested tool. It's recommended for primer trimming anyway, so you can easily pipe the steps and do both demultiplexing-->primer trimming at once if you want.

Edit: I read the question too quickly and confused demultiplexing and dereplication in a previous version of this answer.

[GenoMax]

dereplication is not the same thing as demultiplexing.

DADA2 tutorial expects the samples to be demultiplexed before starting.