Long Run Time for Qiime DADA2 Paired-End Denoising

benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution

http://benjjneb.github.io/dada2/

GNU Lesser General Public License v3.0

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Long Run Time for Qiime DADA2 Paired-End Denoising #2058

Open zbaida-achraf opened 1 week ago

zbaida-achraf commented 1 week ago

Hello, I’m currently working with 96 paired-end patient samples (192 files in total, totaling 66 GB). When I run DADA2, the process takes about a month to complete. My virtual machine is equipped with 32 threads and 128 GB of memory.

benjjneb commented 5 days ago

You can reduce run-time by filtering more stringently and by reducing the amount of data you use to learn the error step.