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/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001}]
              [--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

   optional arguments:
       -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
       {Auto,RAB204/RAB214,PBC001,NBD103/NBD104,RAB214,RPB004/RLB001,NBD114,NBD104/NBD114,PBK004/LWB001,DUAL,RAB204,RBK004,PBC096,RBK001,VMK001},
       --kit
       {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)

       --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

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.