table of contents
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:¶
- -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:¶
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.
April 2020 | qcat 1.1.0 |