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>