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QCAT(1) User Commands 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/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:

show this help message and exit
show program's version number and exit
Print debug information
Don't print summary

General settings:

Barcoded read file
If specified, qcat will demultiplex reads to this folder
Output file trimmed reads will be written to (default: stdout).
Minimum barcode score. Barcode calls with a lower score will be discarded. Must be between 0 and 100. (default: 60)
Search for adapters in the whole read
Number of threads. Only works with in guppy mode
Reads short than <min-read-length> after trimming will be discarded.
Prints a tsv file containing barcode information each read to stdout.
Remove adapter and barcode sequences from reads.
Sequencing kit. Specifying the correct kit will improve sensitivity and specificity and runtime (default: auto)
List all supported kits

Demultiplexing modes:

Use Guppy's demultiplexing algorithm (default: false)
Use EPI2ME's demultiplexing algorithm (default: true)
Use dual barcoding algorithm
Use simple demultiplexing algorithm. Only looks for barcodes, not for adapter sequences. Use only for testing purposes!

EPI2ME options (only valid with --epi2me):

Don't use information from multiple reads for kit detection (default: false)
Filter rare barcode calls when run in batch mode

Simple options (only valid with --simple):

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.

April 2020 qcat 1.1.0