evaluate_kmers

(Required). Character.
A vector containing all unique sequences in the data set.
Only A/C/G/T allowed.

seqs

(Required). A <code>numeric(1)</code>. The size of the kmer to test (eg. 5-mer).

kmer_size

(Required). Numeric matrix (4x4).
The score matrix used during the alignment. Coerced to integer.

score

(Required). A <code>numeric(1)</code> giving the gap penalty for alignment. Coerced to integer.

(Required). A <code>numeric(1)</code> giving the band-size for the NW alignments.

band

(Required). A <code>numeric(1)</code> giving the (maximum) number of
pairwise alignments to do.

max_aligns


Generate the kmer-distance and the alignment distance from the
  given set of sequences.


The dada2 package provides "OTU picking" functionality, but instead
of picking OTUs the DADA2 algorithm exactly infers samples sequences. The dada2
pipeline starts from demultiplexed fastq files, and outputs inferred sample
sequences and associated abundances after removing substitution and chimeric
errors. Taxonomic classification is also available via a native implementation
of the RDP classifier method.

Benjamin Callahan

dada2

Accurate, high-resolution sample inference from amplicon
sequencing data

evaluate_kmers function

Generate the kmer-distance and the alignment distance from the
  given set of sequences.

evaluate_kmers: Generate the kmer-distance and the alignment distance from the given set of sequences.

Description

Usage

Arguments

Value

Examples