Variable length amplicons #66
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Special value of trunc_len=0 turns off truncation and length filtering, allowing variable length amplicons. Also migrated to the multithreaded filterAndTrim for filtering.
Special value of trunc_len_f=0/trunc_len_r=0 turns off truncation and length filtering, Added minLen=10 to denoise-paired and denoise-single. Document this?
thermokarst
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For now just revert the updates to multithreaded filtering, as I’m failing to solve the Travis issue, in service of getting the variable-length functionality merged in.
benjjneb
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This adds support for variable length amplicons. Setting trunc-len/trunc-len-f/trunc-len-r to zero turns off truncation, and everything else proceeds as normal. Truncation to a common length is still recommended for most use-cases (eg. 16S) but for loci like ITS it is sometimes strongly desirable to allow amplicons of variable length, and that should now be supported. |
benjjneb
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ebolyen
approved these changes
Jun 12, 2017
| seqtab <- removeBimeraDenovo(seqtab, method=chimeraMethod, minFoldParentOverAbundance = minParentFold, multithread=multithread) | ||
| } else if(chimeraMethod == "consensus") { | ||
| seqtab <- removeBimeraDenovo(seqtab, method=chimeraMethod, minFoldParentOverAbundance = minParentFold, multithread=multithread) | ||
| if(chimeraMethod %in% c("pooled", "consensus")) { |
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%in%
That's a very interesting spelling.
Thanks! This is much cleaner than what I had done to your R code.
| # Ex: 240 | ||
| # | ||
| # 7) truncLenR - The position at which to truncate reverse reads. Reverse reads shorter | ||
| # than truncLenR will be discarded. | ||
| # Special values: 0 - no truncation or length filtering. |
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Looks like 0 is already a supported value by the code! 👍
gregcaporaso
approved these changes
Jun 12, 2017
This was referenced Jun 26, 2017
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This adds support for variable length amplicons #64
It also adds the multithreaded filtering implemented in dada2 package version 1.4. However, that part is causing some Travis failures I'm having trouble figuring out...