DADA2

This is a workflow to run the DADA2¹ (v1.26.0) software for amplicon data. It currently runs the following DADA2 functions under the hood:

• filterAndTrim for filtering and trimming sequence files
• derepFastq for dereplication
• learnErrors to learn the error rates from the data
• dada the main DADA2 function, to infer sample composition
• mergePairs to merge paired-end reads
• makeSequenceTable to build the per-sample sequence table
• removeBimeraDenovo to remove sequencing chimeras
• assignTaxonomy and addSpecies for taxonomic classification of ASVs

The workflow outputs two data files, one corresponding to the per-sequence table after chimera removal (asv_table.csv) and one for the taxonomic classification (species_table.csv)

Footnotes

1. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016). “DADA2: High-resolution sample inference from Illumina amplicon data.” Nature Methods, 13, 581-583. https://doi.org/10.1038/nmeth.3869. ↩