dada2

Estimate error rates from transition counts in PacBio CCS data.

Add species-level annotation to a taxonomic table.

Taxonomic assignment to the species level by exact matching.

Classifies sequences against reference training dataset.

Change concatenation of dada-class objects to list construction.

Change concatenation of derep-class objects to list construction.

Combine together sequences that are identical up to shifts and/or length.

High resolution sample inference from amplicon data.

The object class returned by dada

DADA2 package

A class representing dereplicated sequences

derepFasta creates a derep-class object from a fasta file, by creating a corresponding fastq file with a uniform quality score and calling derepFastq.

Read in and dereplicate a fastq file.

An empirical error matrix.

An empirical error matrix.

Filter and trim a fastq file.

Filters and trims paired forward and reverse fastq files.

Filter and trim fastq file(s).

Get DADA options

Extract already computed error rates.

Get vector of sequences from input object.

Get the uniques-vector from the input object.

Inflates an error rate matrix by a specified factor, while accounting for saturation.

Determine if input sequence is a bimera of putative parent sequences.

Identify bimeras from collections of unique sequences.

Identify bimeras in a sequence table.

Determine if input sequence(s) match the phiX genome.

Identify sequences that are identical to a more abundant sequence up to an overall shift.

Learns the error rates from an input list, or vector, of file names or a list of derep-class objects.

Use a loess fit to estimate error rates from transition counts.

Construct a sample-by-sequence observation matrix.

This function creates the dada2 assignSpecies fasta file for the RDP from the RDP's _Bacteria_unaligned.fa file.

This function creates the dada2 assignSpecies fasta file for Silva from the SILVA_[VERSION]_SSURef_tax_silva.fasta file

This function creates the dada2 assignTaxonomy training fasta for the RDP trainset .fa file

DEPRECATED in favor of 'makeTaxonomyFasta_SilvaNR“

This function creates the dada2 assignTaxonomy training fasta for the official Silva NR99 release files. If 'include.species'=TRUE, a 7th taxonomic level (species) will be added based on the Genus species binomial in the Silva taxonomy string, if present and valid.

Merge denoised forward and reverse reads.

Merge two or more sample-by-sequence observation matrices.

Deactivate renaming of dada-class objects.

Deactivate renaming of derep-class objects.

Estimate error rates for each type of transition while ignoring quality scores.

Needleman-Wunsch alignment.

Hamming distance after Needlman-Wunsch alignment.

Plot sequence complexity profile of a fastq file.

Plot observed and estimated error rates.

Plot quality profile of a fastq file.

Internal tables function

Reverse complement DNA sequences.

Remove bimeras from collections of unique sequences.

Removes primers and orients reads in a consistent direction.

Determine if input sequence(s) are low complexity.

Set DADA options

method extensions to show for dada2 objects.

An empirical error matrix.

The named integer vector format used to represent collections of unique DNA sequences.

Write a uniques vector to a FASTA file

Writes a named character vector of DNA sequences to a fasta file. Values are the sequences, and names are used for the id lines.