Do you think centrifuge would be successful at classifying 16S reads from Oxford Nanopore? The nanopore reads cover the entire 16S gene (1522bp) but have a high error rate (10-15%). Have you tried using centrifuge of nanopore 16S classification and would you recommend this approach?
I'm interested in developing my own pipeline for 16S classification of nanopore reads instead of using the Oxford Nanopore webservice (developed by Metrichor). I believe that Metrichor is using centrifuge for classification of whole genome sequencing data for metagenomics samples (called What's in my pot? (WIMP)).
Piplopp
commented
6 years ago
Do you think centrifuge would be successful at classifying 16S reads from Oxford Nanopore? The nanopore reads cover the entire 16S gene (1522bp) but have a high error rate (10-15%). Have you tried using centrifuge of nanopore 16S classification and would you recommend this approach?
I'm interested in developing my own pipeline for 16S classification of nanopore reads instead of using the Oxford Nanopore webservice (developed by Metrichor). I believe that Metrichor is using centrifuge for classification of whole genome sequencing data for metagenomics samples (called What's in my pot? (WIMP)).
Thank you for any advice you could offer.