With DADA2, what happens to reads that don't merge?

[colinbrislawn (Colin J Brislawn)]

There is an option to 'just concatenation' in DADA2, but it's not included in the Qiime2 plugin.

So why are we missing this feature?

Well, it turns out that it breaks most other programs downstream:

Dada2 - option - justConcatenate

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 optio…

Expose `fastq_join` command to concatenate (not merge) PE reads

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are pair-ends 2*150
It's 313 long amplicon.

Read1 |--------------->                 150
Read2                 <---------------| 150
amp   |-------------------------------| 313
gap                   ^ 13 bp, so close!

You can select settings so your reads can join, or just use the Fordard for Reverse reads for DADA2 analysis, like a single-end run!