Command Line Interface

Demultiplex any number of FASTA or a FASTQ files based on a list of barcodes

usage: demultiplex [-h] [-v] {guess,demux,match} ...

Positional Arguments

subcommand

Possible choices: guess, demux, match

Named Arguments

-v

show program’s version number and exit

Sub-commands:

guess

Retrieve the most frequent barcodes.

demultiplex guess [-h] [-r] [--format {normal,x,umi,unknown}] [-s START]
                  [-e END] [-o OUTPUT] [-n SAMPLE_SIZE] [-f] [-t THRESHOLD]
                  INPUT

Positional Arguments

INPUT

input file

Named Arguments

-r

extract the barcodes from the read

Default: False

--format

Possible choices: normal, x, umi, unknown

provdide the header format

-s

start of the selection

-e

end of the selection

-o

output file

Default: -

-n

sample size

Default: 1000000

-f

select on frequency instead of a fixed amount

Default: False

-t

threshold for the selection method

Default: 12

demux

Demultiplex any number of files given a list of barcodes.

demultiplex demux [-h] [-r] [--format {normal,x,umi,unknown}] [-s START]
                  [-e END] [-m MISMATCH] [-d] [-p PATH]
                  BARCODES INPUT [INPUT ...]

Positional Arguments

BARCODES

barcodes file

INPUT

input files

Named Arguments

-r

extract the barcodes from the read

Default: False

--format

Possible choices: normal, x, umi, unknown

provdide the header format

-s

start of the selection

-e

end of the selection

-m

number of mismatches

Default: 1

-d

use Levenshtein distance

Default: False

-p

output directory

Default: “.”

match

Demultiplex one file given a list of barcode tuples.

demultiplex match [-h] [-m MISMATCH] [-d] [-p PATH] [-f] [-D]
                  BARCODES INPUT [INPUT ...]

Positional Arguments

BARCODES

barcodes file

INPUT

input files

Named Arguments

-m

number of mismatches

Default: 1

-d

use Levenshtein distance

Default: False

-p

output directory

Default: “.”

-f

write multiple matches to separate files

Default: False

-D

directional input data

Default: False

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