align: Perform Smith-Waterman alignment of a read against a...

In ssw: Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD

Perform Smith-Waterman alignment of a read against a reference sequence

Description

Perform Smith-Waterman alignment of a read against a reference sequence

Usage

align(
  read,
  reference,
  gap_open = 3L,
  gap_extension = 1L,
  start_idx = 0L,
  end_idx = 0L,
  match_score = 2L,
  mismatch_penalty = 2L
)

Arguments

read	A character string of the read.
reference	A character string of the reference.
gap_open	Penalty for opening a gap. Default is 3.
gap_extension	Penalty for extending a gap. Default is 1.
start_idx	Index to start the alignment search. Default is 0.
end_idx	Index to end the alignment search. The default value 0 means using the entire reference length.
match_score	An integer for scoring matches, ranging from 0 to 255. Default is 2.
mismatch_penalty	An integer for mismatch penalties, ranging from 0 to 255. Default is 2.

Value

A list of class ssw containing the ssw aligner object and the alignment results.

Examples

a <- align("ACGT", "TTTTACGTCCCCC")
a
a$alignment$optimal_score
a$alignment$sub_optimal_score

ssw documentation built on Sept. 18, 2024, 9:07 a.m.