- dada2 assign-species
assignSpecies uses exact string matching against a reference database to assign Genus species binomials.
- dada2 filter-trim
Filter and trim fastq file(s).
- dada2 add-species
load in an exact match species training set such as silva_species_assignment_v128.fa.gz for ASVs
- dada2 remove-chimeras
Remove artefactual reads that map to two different parent sequences
- dada2 learn-errors
Learns the error rates from an input list, or vector, of files
- dada2 merge-pairs
Merge denoised forward and reverse reads
- dada2 assign-taxonomy
assignTaxonomy implements the RDP naive Bayesian classifier method described in Wang et al. 2007.
- dada2 collapse-nomismatch
ombine together sequences that are identical up to shifts and/or length
- dada2 dereplicate-fastq
Dereplication combines all identical sequencing reads into into unique sequences with a corresponding abundance equal to the number of reads with that unique sequence. Dereplication substantially reduces computation time by eliminating redundant comparisons.
- dada2 make-table
Construct a sample-by-sequence observation matrix.