Barcode Discovery

This program searches for possible barcodes and barcode enzyme combinations.
Designed for the discovery of sequencing errors, or unused barcodes when a large proportion of the demultiplex is undetermined.

Mandatory parameters:

• -f1 the name of the input file (mandatory)
  Optional parameters:
• -min the minimum length of the barcode (standard 6)
• -max the maximum length of the barcode (standard 10)
• -gzip use gzip files as input and output (standard false)
• -o the output directory (standard the directory of execution)
• -ea Add enzymes from the given file (keeps the standard enzymes, and add the new) (enzyme file: no header, enzyme name tab cutsites (multiple cutsites are comma separeted)) (example: enzyme ApeKI and restriction site G^CWGC: "ApeKI \tab CAGC,CTGC") (only use once, not use -er)
• -er Replace enzymes from the given file (do not keep the standard enzymes) (enzyme file: no header, enzyme name tab cutsites (multiple cutsites are comma separeted)) (example: enzyme ApeKI and restriction site G^CWGC: "ApeKI \tab CAGC,CTGC") (only use once, not use -ea)
• -barmin The minimum occurance of a barcode before it is shown in the results (standard: 200)
• -barmax The maximum occurance of barcodes shown in the output (increasing this number will increase ram usage, but gives a slightly better result) (standard: 100)
• -barmis The percentage of mismatches that may occure between barcodes (integer between 1 and 10) (standard: 10)