---
name: "qcat"
section: "1"
platform: "linux"
package: "qcat"
version: "1.1.0-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/qcat"
---

# qcat(1)

demultiplexing Oxford Nanopore reads from FASTQ files

## NAME

qcat - demultiplexing Oxford Nanopore reads from FASTQ files

## DESCRIPTION

usage: qcat \[-h\] \[-V\] \[-l LOG\] \[--quiet\] \[-f FASTQ\] \[-b BARCODE\_DIR\]

-

  \[-o OUTPUT\] \[--min-score MIN\_QUAL\] \[--detect-middle\] \[-t THREADS\] \[--min-read-length MIN\_LENGTH\] \[--tsv\] \[--trim\] \[-k {Auto,RAB204,RPB004/RLB001,NBD104/NBD114,\
    RAB204/RAB214,VMK001,NBD103/NBD104,PBC001,PBK004/LWB001,\
    RAB214,RBK004,PBC096,RBK001,NBD114,DUAL}\] \[--list-kits\] \[--guppy \| **--epi2me** \| **--dual** \| **--simple\]** \[--no-batch\] \[--filter-barcodes\] \[--simple-barcodes SIMPLE\_BARCODES\]

Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files

### 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