dada2
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benjjneb
Accurate sample inference from amplicon data with single nucleotide resolution
- Symbols are still maintained as they are used in a mnumber of places. - SSE should be set to 0 for non-x86_x64 so the code paths expecting SSE should...
This change reduces the amount of memory used by assignTaxonomy by allocating a constant size of arrays before dispatching parallel tasks. ## Rationale I was reviewing dada2 wrappers for MicrobiomeDB,...
Dear Mr. Callahan, I am running the DADA2 pipeline on a large number of samples using your big data tutorial for PE reads. The last 3 lines of the section:...
The `dada()` verbose output typically ends with something like ``` selfConsist step 2> ``` where the ">" is the prompt. It seems to be happening because the last printed line...
assignTaxonomy() raises "random_device: rdseed failed" error when used in multi threaded mode (and single threaded sometimes). It seems to be caused by an error in recent versions of `libstdc++` (gcc...
The SILVA r138 classifier has just been released on the [DECIPHER](http://www2.decipher.codes/Downloads.html) website. Please consider upgrading the DADA2 [tutorial](https://benjjneb.github.io/dada2/tutorial.html) to reflect this version. Thanks!
Hi, Similiar to #432 I get a warning on an integer overflow when running `dada` ``` dadaForward
The LRAS manuscript reproducible markdowns are fine, but a dedicated tutorial workflow is much preferred.
I had a problem with orient.fwd because my UMI primer goes like: DBHVDBVHDHBVACBTRGTGTGAATTGCAGRATC I was very sad this did not support any IUPAC characters. I made a duct-tape solution by...
Hi! I am confused as to why many of the dada2 functions unlist their return value, if there is only one input/output object, e.g.: * https://github.com/benjjneb/dada2/blob/963f4e023023bc528177a2c04ab7f1ae5332461c/R/dada.R#L478 * https://github.com/benjjneb/dada2/blob/963f4e023023bc528177a2c04ab7f1ae5332461c/R/sequenceIO.R#L114 * https://github.com/benjjneb/dada2/blob/963f4e023023bc528177a2c04ab7f1ae5332461c/R/paired.R#L199...
