Q2-ITSxpress: A tutorial on a QIIME 2 plugin to trim ITS sequences

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Thanks for all the feedback @gregcaporaso @benjjneb and @Nicholas_Bokulich

So I will:

  1. Add add an option to export unpaired reads for Dada2 in the format SampleData[PairedEndSequencesWithQuality]

  2. Add an option to export SampleData[JoinedSequencesWithQuality] for Deblur and

  3. Remove the ability to export SampleData[SequencesWithQuality]

To answer @Nicholas_Bokulich's question:

Does ITSxpress work on single-end reads? If so, why not use it to trim ITS in forward/reverse separately, and then denoise with dada2?

That could be done but it would more than double the running time and would not allow validation that the beginning and end are present for the selected ITS region. After thinking about it more I realised I could calculate the 5' trimming positions of the reads from the merged sequences. so I will do that instead.

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