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!
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.
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).
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.