.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.5.
.TH QCAT "1" "November 2022" "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,RPB004/RLB001,NBD104/NBD114,
 RAB204/RAB214,VMK001,NBD103/NBD104,PBC001,PBK004/LWB001,
 RAB214,RBK004,PBC096,RBK001,NBD114,DUAL}]
[\-\-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 "options:"
.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, \fB\-\-kit\fR {Auto,RAB204,RPB004/RLB001,NBD104/NBD114,RAB204/RAB214,
 VMK001,NBD103/NBD104,PBC001,PBK004/LWB001,RAB214,RBK004,PBC096,
 RBK001,NBD114,DUAL}
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