QCAT(1)

NAME
qcat - demultiplexing Oxford Nanopore reads from FASTQ files

DESCRIPTION
usage: qcat [-h] [-V] [-l LOG] [--quiet] [-f FASTQ] [-b BARCODE_DIR]

    [-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 | --epi2me | --dual | --simple] [--no-batch] [--filter-barcodes] [--simple-barcodes SIMPLE_BARCODES]

Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files

  options:

-h, --help
    show this help message and exit

-V, --version
    show program's version number and exit

-l LOG, --log LOG
    Print debug information

--quiet
    Don't print summary

  General settings:

-f FASTQ, --fastq FASTQ
    Barcoded read file

-b BARCODE_DIR, --barcode_dir BARCODE_DIR
    If specified, qcat will demultiplex reads to this folder

-o OUTPUT, --output OUTPUT
    Output file trimmed reads will be written to (default: stdout).

--min-score MIN_QUAL
    Minimum barcode score. Barcode calls with a lower score will be discarded. Must be between 0 and 100. (default: 60)

--detect-middle
    Search for adapters in the whole read

-t THREADS, --threads THREADS
    Number of threads. Only works with in guppy mode

--min-read-length MIN_LENGTH
    Reads short than <min-read-length> after trimming will be discarded.

--tsv
    Prints a tsv file containing barcode information each read to stdout.

--trim
    Remove adapter and barcode sequences from reads.

-k, --kit {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)

--list-kits
    List all supported kits

  Demultiplexing modes:

--guppy
    Use Guppy's demultiplexing algorithm (default: false)

--epi2me
    Use EPI2ME's demultiplexing algorithm (default: true)

--dual
    Use dual barcoding algorithm

--simple
    Use simple demultiplexing algorithm. Only looks for barcodes, not for adapter sequences. Use only for testing purposes!

  EPI2ME options (only valid with --epi2me):

--no-batch
    Don't use information from multiple reads for kit detection (default: false)

--filter-barcodes
    Filter rare barcode calls when run in batch mode

  Simple options (only valid with --simple):

--simple-barcodes SIMPLE_BARCODES
    Use 12 (standard) or 96 (extended) barcodes for demultiplexing