Qiime2 with IonTorrent data

Hey guys, a question before starting my analysis…I have IonTorrent .fastq files that the guy from the sequencing provider gave me. I have 40 files for the 40 individuals of the analysis, one file for each with single-end reads. I do not have any text file with barcodes.
Checking the import data tutorial I think the EMP protocol or the Casava will not work. Is this right? The unique alternative is to create the .fastq manifest?


Correct. EMP is a multiplexed format. Casava 1.8 is specific to Illumina files in that format. Manifest is the catch-all format for demultiplexed files.

There are various other posts on this forum about analyzing ion torrent data — you may want to check those out to see how other users have dealt with their data for importing and post-importing processing.

I hope that helps!

Thanks Nicholas. I was able to create the manifest-file and import the data!! Great achievement for the first day as I am not a bioinformatic at all.

I will keep bodering with more questions for sure



An off-topic reply has been split into a new topic: How to trim and quality filter ion torrent data?

Please keep replies on-topic in the future.

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