qcat1

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