Classifies sequences against reference training dataset.
An empirical error matrix.
An empirical error matrix.
Map denoised sequence to each read.
Merge forward and reverse reads after DADA denoising,
even if reads were not originally ordered together.
Use a loess fit to estimate error rates from transition counts.
An empirical error matrix.
Inflates an error rate matrix by a specified factor, while accounting for saturation.
Get DADA options
Internal tables function
An empirical error matrix.
Plot observed error rates after denoising.
Plot quality profile of a fastq file.
The named integer vector format used to represent collections of unique DNA sequences.
method extensions to show for dada2 objects.
Combine together sequences that are identical up to shifts and/or length.
An empirical error matrix.
Identify sequences that are identical to a more abundant sequence up to an
overall shift.
Get vector of sequences from input object.
A class representing dereplicated sequences
Determine if input sequence is a bimera of putative parent sequences.
An empirical error matrix.
Read in and dereplicate a fastq file.
The object class returned by dada Write a uniques vector to a FASTA file
Needlman-Wunsch alignment.
Hamming distance after Needlman-Wunsch alignment.
Identify bimeras from collections of unique sequences.
Filter and trim a fastq file.
High resolution sample inference from amplicon data.
Generate the kmer-distance and the alignment distance from the
given set of sequences.
Determine if input sequence(s) match the phiX genome.
Filters and trims paired forward and reverse fastq files.
An empirical error matrix.
Set DADA options
Remove bimeras from collections of unique sequences.
DADA2 package
Construct a sample-by-sequence observation matrix.
Merge denoised forward and reverse reads.
plotComplementarySubstitutions
Plot Substitution Pairs from DADA Result
Get the uniques-vector from the input object.