Command Line Interface

Design and test NGS barcodes.

usage: barcode [-h] [-v] {make,test} ...

Positional Arguments

subcommand

Possible choices: make, test

Named Arguments

-v

show program’s version number and exit

Sub-commands:

make

Make a set of barcodes, filter them for mononucleotide stretches and for

distances with other barcodes.

barcode make [-h] [-d DISTANCE] [-H] [-l LENGTH] [-s STRETCH] OUTPUT

Positional Arguments

OUTPUT

output file

Named Arguments

-d

minimum distance between the barcodes (int default=3)

Default: 3

-H

use Hamming distance

Default: False

-l

lenght of the barcodes (int default=8)

Default: 8

-s

maximum mononucleotide stretch length (int default=2)

Default: 2

test

Test a set of barcodes.

barcode test [-h] [-d DISTANCE] [-H] [-o OUTPUT] INPUT

Positional Arguments

INPUT

input file

Named Arguments

-d

minimum distance between the barcodes (int default=3)

Default: 3

-H

use Hamming distance

Default: False

-o

list of good barcodes

Copyright (c) Jeroen F.J. Laros <J.F.J.Laros@lumc.nl>