.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.13.
.TH QCAT "1" "April 2020" "qcat 1.1.0" "User Commands"
.SH NAME
qcat \- demultiplexing Oxford Nanopore reads from FASTQ files
.SH DESCRIPTION
usage: qcat [\-h] [\-V] [\-l LOG] [\-\-quiet] [\-f FASTQ] [\-b BARCODE_DIR]
.IP
[\-o OUTPUT] [\-\-min\-score MIN_QUAL] [\-\-detect\-middle] [\-t THREADS]
[\-\-min\-read\-length MIN_LENGTH] [\-\-tsv] [\-\-trim]
[\-k {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}]
[\-\-list\-kits] [\-\-guppy | \fB\-\-epi2me\fR | \fB\-\-dual\fR | \fB\-\-simple]\fR
[\-\-no\-batch] [\-\-filter\-barcodes]
[\-\-simple\-barcodes SIMPLE_BARCODES]
.PP
Python command\-line tool for demultiplexing Oxford Nanopore reads from FASTQ files
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
show program's version number and exit
.TP
\fB\-l\fR LOG, \fB\-\-log\fR LOG
Print debug information
.TP
\fB\-\-quiet\fR
Don't print summary
.SS "General settings:"
.TP
\fB\-f\fR FASTQ, \fB\-\-fastq\fR FASTQ
Barcoded read file
.TP
\fB\-b\fR BARCODE_DIR, \fB\-\-barcode_dir\fR BARCODE_DIR
If specified, qcat will demultiplex reads to this
folder
.TP
\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
Output file trimmed reads will be written to (default:
stdout).
.TP
\fB\-\-min\-score\fR MIN_QUAL
Minimum barcode score. Barcode calls with a lower
score will be discarded. Must be between 0 and 100.
(default: 60)
.TP
\fB\-\-detect\-middle\fR
Search for adapters in the whole read
.TP
\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
Number of threads. Only works with in guppy mode
.TP
\fB\-\-min\-read\-length\fR MIN_LENGTH
Reads short than <min\-read\-length> after trimming will
be discarded.
.TP
\fB\-\-tsv\fR
Prints a tsv file containing barcode information each
read to stdout.
.TP
\fB\-\-trim\fR
Remove adapter and barcode sequences from reads.
.TP
\fB\-k\fR {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}, \fB\-\-kit\fR {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}
Sequencing kit. Specifying the correct kit will
improve sensitivity and specificity and runtime
(default: auto)
.TP
\fB\-\-list\-kits\fR
List all supported kits
.SS "Demultiplexing modes:"
.TP
\fB\-\-guppy\fR
Use Guppy's demultiplexing algorithm (default: false)
.TP
\fB\-\-epi2me\fR
Use EPI2ME's demultiplexing algorithm (default: true)
.TP
\fB\-\-dual\fR
Use dual barcoding algorithm
.TP
\fB\-\-simple\fR
Use simple demultiplexing algorithm. Only looks for
barcodes, not for adapter sequences. Use only for
testing purposes!
.SS "EPI2ME options (only valid with --epi2me):"
.TP
\fB\-\-no\-batch\fR
Don't use information from multiple reads for kit
detection (default: false)
.TP
\fB\-\-filter\-barcodes\fR
Filter rare barcode calls when run in batch mode
.SS "Simple options (only valid with --simple):"
.TP
\fB\-\-simple\-barcodes\fR SIMPLE_BARCODES
Use 12 (standard) or 96 (extended) barcodes for
demultiplexing
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.