qcat - demultiplexing Oxford Nanopore reads from FASTQ files
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
- -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
- --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!
- --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
This manpage was written by Andreas Tille for the Debian
distribution and
can be used for any other usage of the program.