What versions of DADA2 are available for R?

If you don’t already have it, see the dada2 installation instructions. Older versions of this workflow associated with previous release versions of the dada2 R package are also available: 1.6, 1.8, 1.12, . The data we will work with are the same as those used in the mothur MiSeq SOP.

What is maxN in DADA2?

We’ll use standard filtering parameters: maxN=0 (DADA2 requires no Ns), truncQ=2 and maxEE=2. The maxEE parameter sets the maximum number of “expected errors” allowed in a read, which is a better filter than simply averaging quality scores.

Why is dereplication important in the DADA2 pipeline?

Dereplication substantially reduces computation time by eliminating redundant comparisons. Dereplication in the DADA2 pipeline has one crucial addition from other pipelines: DADA2 retains a summary of the quality information associated with each unique sequence.

Why are the reverse reads in DADA2 so bad?

The reverse reads are of significantly worse quality, especially at the end, which is common in Illumina paired-end sequencing. This isn’t too worrisome, DADA2 incorporates quality information into its error model which makes the algorithm is robust to lower quality sequence, but trimming as the average qualities crash is still a good idea.

https://www.youtube.com/watch?v=j9W354GOKA0

Are there any alternatives to the DADA2 its workflow?

See the DADA2 ITS workflow for more information Alternatives: Zymo Research has recently developed a tool called Figaro that can help you choose DADA2 truncation length parameters: https://github.com/Zymo-Research/figaro#figaro

How many true sequence variants does the DADA2 algorithm infer?

The DADA2 algorithm inferred 128 true sequence variants from the 1979 unique sequences in the first sample.

https://www.youtube.com/watch?v=lmAT83KDo9Q