16S microbial analysis of Nanopore data with Mothur

Hi there,

Is Mothur compatible with Nanopore sequencing data? if not, what can I do to circumvent the first step (pairing data and make contig.s)?

Note: We have 16S data from Nanopore sequencing. We need to obtain OTU tables for beta diversity and relative abundances. We hope to use Mothur to analyze our Nanopore data.

Thank you.


I have yet to see anything that suggests nanopore data is of sufficient quality to do things like OTUs or ASVs. If you or anyone else has mock community data with nanopore data, I’d love to play with it. You can always use trim.seqs to do quality base trimming and to remove any barcodes and primers.


Thank you so much for your feedback. This is very meaningful.

We will try another way doing analysis for 16S Nanopore data.



I will start playing with nanopore data in the coming month, I will keep you posted. With luck I will be able to do nanopore reads on MiSeq sequenced samples as well as mock communities.

Thank you so much. Expect it.