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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. ↩