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Add ability to join paired reads #12
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Is there currently a QIIME object for paired fastq files (or lists of paired fastq files)? |
I don't believe that there is. @ebolyen can you confirm? |
There is if I understand the question correctly: |
If that exists already, then adding a paired end workflow should be straightforward. Is there documentation of |
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 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. |
The script run_dada_faster_paired.R was added, and implements paired end functionality. It inputs directories of demultiplexed forward and reverse reads as they come off the Illumina sequencer (i.e. F/R are in matched order for each sample). Output is the sequence table. Multithreading and error estimation from a subet of the data is a part of this workflow. This solves #12 from the R side.
Similar to running dada2 in R it would be nice to have the ability to join paired reads with the q2 plugin
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