How to import Roche 454 pyrosequencing data in QIIME2 without using QIIME1?

[Sparkle]

Hello everyone, I’m new here.
I’m working on .fastq files obtained through Roche454 pyrosequencing. I’d like to denoise them with dada2, by using qiime dada2 denoise-pyro, but I’m having trouble before this step, probably due to file format.

More specifically, I created a .qza file with the parameter --type 'SampleData[SequencesWithQuality] (–type EMPSingleEndSequences gives me an error) but unfortunately the next qiime demux emp-single script doesn’t support the former, but only the latter format EMPSingleEndSequences, making it impossible to continue.

Is there any direct and simple way to import pyrosequencing data in QIIME2 without using QIIME1? I’m asking because the only ways I found online mentioned QIIME1 codes.

Thanks in advance!

[colinbrislawn (Colin J Brislawn)]

Hello @Sparkle! Welcome to the forums.

I think the cutadapt plugin will work well on 454 data. Check out this tutorial and see if it looks like a good fit for your data set.

Demultiplexing and Trimming Adapters from Reads with q2-cutadapt

NOTE This tutorial is a work in progress, and is incomplete at the moment. It demonstrates at a high level some of the methods available in the q2-cutadapt plugin available in QIIME 2 2018.2. Please stay tuned here for additional updates as this tutorial is expanded upon in the coming weeks. Multiplexed reads with the barcodes in the sequence reads can be demultiplexed in QIIME 2 using the q2-cutadapt plugin,…

Colin