Comments (3)
benjjneb
commented on August 18, 2024
Right now the q2 plugin is using the 1.0.3 release of dada2, not the development branch, so multithreading isn't available.
The next dada2 release (1.2) is next month, and will have multithreading. It probably makes the most sense for stability reasons to migrate to the next release before adding multithreading to the plugin.
There are also some modifications to the plugin workflow that would speed things up a lot for larger datasets (basically estimating error rates from a subset of the data).
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benjjneb
commented on August 18, 2024
This depends on #13 (installation of up-to-date dada2 release).
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benjjneb
commented on August 18, 2024
Assumes dada2 1.2+
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Related Issues (20)
- Allow denoise-single to process either reverse or forward reads HOT 3
- Add long-read support HOT 27
- Certain ID schemes can become mixed up with barcodes during sorting HOT 3
- I've gone through tutorials and forums and still don't understand how to select the truncLen and trim parameters in dada2 HOT 1
- denoise-paired: add % merged to stats output
- expose minOverlap parameter HOT 10
- denoise-paired: expose matchIDs parameter HOT 3
- Error in sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) HOT 13
- Update denoise-paired document from minimum overlap 20 > 12nt
- Setting "allowOneOf" and "maxMismatch" parameters in q2/dada2 plugin HOT 1
- dada2 justConcatenate HOT 6
- Update to latest DADA2 for R 4.0 support HOT 1
- dada2 drops samples without reads unfiltered reads from table but not denoising stats. HOT 1
- Restructuring dada2 R/python code
- error while using dada2 in qiime2 HOT 1
- ENH: include error model plots in denoise-* output HOT 3
- Importing DADA2 R rep. sequences into QIIME2 HOT 1
- Can not run qiime dada2 denoise-ccs without primers or adapters HOT 4
- Improve summary for merging paired reads HOT 4
- Add more DADA2 parameters to the wrapper HOT 3
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