nwalign {dada2} | R Documentation

## Needleman-Wunsch alignment.

### Description

This function performs a Needleman-Wunsch alignment between two sequences.

### Usage

    nwalign(
      s1,
      s2,
      match = getDadaOpt("MATCH"),
      mismatch = getDadaOpt("MISMATCH"),
      gap = getDadaOpt("GAP_PENALTY"),
      homo_gap = NULL,
      band = -1,
      endsfree = TRUE,
      vec = FALSE
    )

### Arguments

`s1` | (Required). `character(1)`. The first sequence to align. A/C/G/T only.
`s2` | (Required). `character(1)`. The second sequence to align. A/C/G/T only.
`match` | (Optional). `numeric(1)`. Default is getDadaOpt("MATCH"). The score of a match in the alignment.
`mismatch` | (Optional). `numeric(1)`. Default is getDadaOpt("MISMATCH"). The score of a mismatch in the alignment.
`gap` | (Optional). `numeric(1)`. Default is getDadaOpt("GAP_PENALTY"). The alignment gap penalty. Should be negative.
`homo_gap` | (Optional). `numeric(1)`. Default NULL (no special homopolymer penalty). The alignment gap penalty within homopolymer regions. Should be negative.
`band` | (Optional). `numeric(1)`. Default -1 (no banding). The Needleman-Wunsch alignment can be banded. This value specifies the radius of that band. Set `band = -1` to turn off banding.
`endsfree` | (Optional). `logical(1)`. Default TRUE. Allow unpenalized gaps at the ends of the alignment.
`vec` | (Optional). `logical(1)`. Default FALSE. Use DADA2's vectorized aligner instead of standard DP matrix. Not intended for long sequences (>1kb).

### Value

`character(2)`. The aligned sequences.

### Examples

     sq1 <- "CTAATACATGCAAGTCGAGCGAGTCTGCCTTGAAGATCGGAGTGCTTGCACTCTGTGAAACAAGATA"
     sq2 <- "TTAACACATGCAAGTCGAACGGAAAGGCCAGTGCTTGCACTGGTACTCGAGTGGCGAACGGGTGAGT"
     nwalign(sq1, sq2)
     nwalign(sq1, sq2, band=16)

[Package dada2 version 1.20.0 Index]