Optimize DADA2 setup for Nanopore reads

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1

Hello,

This is my first time using qiime.
I have full-length 16s metagenomics data sequence using MinION Mk1B.

I have imported the single-end sequence to qiime:
qiime tools import
--type 'SampleData[SequencesWithQuality]'
--input-path manifest_16s_dip_rh.tsv
--output-path single-end-demux.qza
--input-format SingleEndFastqManifestPhred33V2

Currently I am in the process of denoising using DADA2
qiime dada2 denoise-single
--i-demultiplexed-seqs single-end-demux.qza
--p-trim-left 0
--p-trunc-len 0
--o-representative-sequences rep-seqs-dada2.qza
--o-table table-dada2.qza
--o-denoising-stats stats-dada2.qza

image
image1883×872 155 KB

statsdada
statsdada1919×884 69.8 KB

Is there any best practice to import nanopore reads and and denoise it using DADA2?
Also how do I produce ASV table from nanopore reads in Qiime

Thanks

2

Hey @zahir,

Based on a quick search of the DADA2 issue tracker, I think this is unlikely to work:

It seems that the general case is there are too small a proportion of "clean" reads for the model to get to work on. And I think that's replicated in your denoising stats, which definitely don't look great.

I think you may be better served by vsearch clustering as an ad-hoc technique, or using another tool and coming back to QIIME 2 post-read processing. I'm sorry that I'm not terribly familiar with this platform, so I don't have any good tool recommendations.

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