isoQC

Description:

This function loads in ABIF files (.ab1 extension) and performs automatic quality trimming in batch mode.

Usage:

isoQC(input = NULL,
  export_html = TRUE,
  export_csv = TRUE,
  export_fasta = TRUE,
  verbose = FALSE,
  exclude = NULL,
  min_phred_score = 20,
  min_length = 200,
  sliding_window_cutoff = NULL,
  sliding_window_size = 15,
  date = NULL,
  files_manual = NULL)

Arguments:

Parameter	Description
input	Path to directory with .ab1 files.
export_html	(Default=TRUE) Output the results as an HTML file.
export_csv	(Default=TRUE) Output the results as a CSV file.
export_fasta	(Default=TRUE) Output the sequences in a FASTA file.
verbose	(Default=FALSE) Output progress while script is running.
exclude	(Default=NULL) For testing purposes only. Excludes files of interest from input directory.
min_phred_score	(Default=20) Do not accept trimmed sequences with a mean Phred score below this cutoff.
min_length	(Default=TRUE) (Default=200) Do not accept trimmed sequences with sequence length below this number.
sliding_window_cutoff	Quality trimming parameter (M2) for wrapping SangerRead function in sangeranalyseR package. If NULL, implements auto cutoff for Phred score (recommended), otherwise set between 1-60.
sliding_window_size	(Default=15) Quality trimming parameter (M2) for wrapping SangerRead function in sangeranalyseR package. Recommended range between 5-30.
date	Set date "YYYY_MM_DD" format. If NULL, attempts to parse date from .ab1 file.
files_manual	(Default=NULL) For testing purposes only. Specify a list of files to run as filenames without extensions, rather than the whole directory format. Primarily used for testing, use at your own risk.