How to import Nanopore 16S data?

Hi there,
I have single-end 16S sequencing data obtained with a MinION (SQK-RAB204) that I’d like to analyze with Qiime2.
I used Albacore for basecalling and demultiplexed into 6 independent fastq files. Similar questions have been asked some time ago, but I couldn’t find a clear pipeline.
For the first step: what is the best way to import this type of data to Qiime2? can I use, for example, “Casava 1.8 single-end demultiplexed fastq”?.
Thanks a lot!

Hi @HectorH,

Sorry for the very delayed response.

I don’t think we have a lot of experience with MinION, but, I think your idea of using the Casava 1.8 format should work fine. You can also give the fastq manifest a shot.

Out of curiousity, what does MinION data look like? It would be cool to be able to support this more directly in QIIME 2.

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thank you @ebolyen ,
I managed to import my data using the manifest:

qiime tools import --type ‘SampleData[SequencesWithQuality]’ --input-path se_33_manifest --output-path single-end-demux.qza --source-format SingleEndFastqManifestPhred33

so probably there is no need to try the Casava format.
I will test now different options for trimming and feature table construction (my reads are about 1.5 kb).


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