Add ability to join paired reads

[johnchase]

Similar to running dada2 in R it would be nice to have the ability to join paired reads with the q2 plugin

[benjjneb]

Is there currently a QIIME object for paired fastq files (or lists of paired fastq files)?

[johnchase]

I don't believe that there is. @ebolyen can you confirm?

[ebolyen]

There is if I understand the question correctly: SampleData[PairedEndSequencesWithQuality] which uses SingleLanePerSamplePairedEndFastqDirFmt as its backing directory format.

[benjjneb]

If that exists already, then adding a paired end workflow should be straightforward.

Is there documentation of SampleData[PairedEndSequencesWithQuality] objects? For example, can it be assumed there are always forward and reverse files for each sample?

[ebolyen]

No real documentation, and we can't yet enforce that there exists a forward and reverse for each sample, but I believe it is our goal to be able to validate that property. That particular directory format does contain a manifest file which maps the sample id to the filepath and direction.

relevant lines for format
manifest definition
q2-demux which manipulates these

These parts of the API (multi-file directory formats) are still very rough around the edges, but we're thinking about ways to make it easier.

[benjjneb]

Added in a1857e5 and b66432d

Assumes dada2 1.2+