stitch {insect}

Paired-end read stitching.

Description

This function aligns forward and reverse reads generated from a 2x amplicon sequencing platform, and produces a consensus sequence with maximum base-call quality scores attached as "quality" attributes.

Usage

stitch(x, y, up = NULL, down = NULL, mindiff = 6, minoverlap = 16)

Arguments

x, y

DNAbin objects with quality attributes (see readFASTQ to generate these objects from fastq text files), representing the forward and reverse reads to be stitched. These objects can be either vectors or lists. In the latter case, the two objects must be equal length.

up, down

forward and reverse primer sequences (either as concatenated character strings or "DNAbin" objects). Either both or neither should be provided (not one or the other).

mindiff

the minimum difference in quality between two different base calls for the higher quality call to be added to the consensus alignment. In cases where the quality differences are less than this threshold, the ambiguity code "N" is added to the consensus sequence. Defaults to 6.

minoverlap

integer giving the minimum number of nucleotides that should be shared between the forward and reverse sequence alignments. Defaults to 16.

Value

a "DNAbin" object or a vector of concatenated character strings, depending on the input.

Author(s)

Shaun Wilkinson

See Also

readFASTQ.

Examples

  ## download and extract example FASTQ file to temporary directory
  td <- tempdir()
  URL <- "https://www.dropbox.com/s/71ixehy8e51etdd/insect_tutorial1_files.zip?dl=1"
  dest <- paste0(td, "/insect_tutorial1_files.zip")
  download.file(URL, destfile = dest, mode = "wb")
  unzip(dest, exdir = td)
  x <- readFASTQ(paste0(td, "/COI_sample1_read1.fastq"), bin = FALSE)
  y <- readFASTQ(paste0(td, "/COI_sample1_read2.fastq"), bin = FALSE)
  z <- stitch(x, y)
  z[1]
  attr(z, "quality")[1]