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,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
- -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
- --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