Dada2 - option - justConcatenate

[JeremyTournayre]

Hello,

I need to add the "justConcatenate" option to dada2.

If I follow the same procedure as this topic which presents how to add the minoverlap option to dada2: Dada2 minimum overlap - #2 by Nicholas_Bokulich, it will be good? (The justConcatenate option is also an argument to the mergePairs function.)

As in the topic mentioned above, how can this option be added on a future update of QIIME2 ?

Bye
Jérémy Tournayre

[Nicholas_Bokulich]

Hi @JeremyTournayre ,

We are not likely to add this option in QIIME 2, as it can introduce some serious issues downstream, e.g., for taxonomic classification. Basically, just concatenating non-overlapping pairs end-to-end can mess up alignments (e.g., for phylogeny building) and kmer profiles (e.g., used for taxonomy classification) because these concatenated reads are artificial constructs. You can read more about these concerns here, also a number of other forum topics that discuss this option:

classification of non-overlapping reads treated with justConcatenate

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