---
name: "readucks"
section: "1"
platform: "linux"
package: "readucks"
version: "0.0.3-5"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/readucks"
---

# readucks(1)

Nanopore read de-multiplexer (read demux -\> readux -\> readucks, innit)

## NAME

readucks - Nanopore read de-multiplexer (read demux -\> readux -\> readucks, innit)

## DESCRIPTION

usage: readucks **-i** INPUT\_PATH \[-o OUTPUT\_DIR\] \[-b\] \[-a\] \[-e\] \[-s\] \[-m MODE\]

-

  \[-p PREFIX\] \[-t THREADS\] \[-n NUM\_READS\_IN\_BATCH\] \[--check\_reads CHECK\_READS\] \[--adapter\_threshold ADAPTER\_THRESHOLD\] \[-v VERBOSITY\] \[--require\_two\_barcodes\] \[--report\_alternate\_call\] \[--native\_barcodes\] \[--pcr\_barcodes\] \[--rapid\_barcodes\] \[--limit\_barcodes\_to LIMIT\_BARCODES\_TO \[LIMIT\_BARCODES\_TO ...\]\] \[--threshold THRESHOLD\] \[--secondary\_threshold SECONDARY\_THRESHOLD\] \[--score\_diff SCORE\_DIFF\] \[--scoring\_scheme SCORING\_SCHEME\] \[-h\] \[--version\]

Readucks: a simple demuxing tool for nanopore data.

### Main options:

- **-i** INPUT\_PATH, **--input** INPUT\_PATH

  FASTQ of input reads or a directory which will be recursively searched for FASTQ files (required).

- **-o** OUTPUT\_DIR, **--output\_dir** OUTPUT\_DIR

  Output directory (default: working directory)

- **-b**, **--bin\_barcodes**

  Reads will be binned based on their barcode and saved to separate files. (default: False)

- **-a**, **--annotate\_files**

  Writes a CSV file for each input file containing barcode calls for each read. (default: False)

- **-e**, **--extended\_info**

  Writes extended information about barcode calls. (default: False)

- **-s**, **--summary\_info**

  Writes another file with information about barcode calls. (default: False)

- **-m** MODE, **--mode** MODE

  Demuxing mode, one of \["stringent","lenient", "porechop"\]. (default: porechop)

- **-p** PREFIX, **--prefix** PREFIX

  Optional prefix to file names

- **-t** THREADS, **--threads** THREADS

  The number of threads to use (1 to turn off multithreading) (default: 2)

- **-n** NUM\_READS\_IN\_BATCH, **--num\_reads\_in\_batch** NUM\_READS\_IN\_BATCH

  The number of reads to process (and hold in memory) at a time (default: 200)

- **--check\_reads** CHECK\_READS

  Number of barcodes to classify before filtering barcode set (default: 1000)

- **--adapter\_threshold** ADAPTER\_THRESHOLD

  Identity required for a barcode to be included after filtering (default: 90)

- **-v** VERBOSITY, **--verbosity** VERBOSITY

  Level of output information: 0 = none, 1 = some, 2 = lots (default: 1)

### Demuxing options:

- **--require\_two\_barcodes**

  Match barcodes at both ends of read (default single)

- **--report\_alternate\_call**

  Reports double/single barcode call to csv in single/double barcoding mode (default: False)

- **--native\_barcodes**

  Only attempts to match the 24 native barcodes (default)

- **--pcr\_barcodes**

  Only attempts to match the 96 PCR barcodes (default: False)

- **--rapid\_barcodes**

  Only attempts to match the 12 rapid barcodes (default: False)

- **--limit\_barcodes\_to** LIMIT\_BARCODES\_TO \[LIMIT\_BARCODES\_TO ...\]

  Specify a list of barcodes to look for (numbers refer to native, PCR or rapid)

### Barcode search settings:

-

  Settings for how to search for and call barcodes

- **--threshold** THRESHOLD

  A read must have at least this percent identity to a barcode (default: 75)

- **--secondary\_threshold** SECONDARY\_THRESHOLD

  The second barcode must have at least this percent identity (and match the first one) (default: 65)

- **--score\_diff** SCORE\_DIFF

  The second barcode must have at least this percent identity (and match the first one) (default: 5)

- **--scoring\_scheme** SCORING\_SCHEME

  Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend (default: 3,-6,-5,-2)

### Help:

- **-h**, **--help**

  Show this help message and exit

- **--version**

  Show program's version number and exit

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.