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