---
name: "unicycler_scrub"
section: "1"
platform: "linux"
package: "unicycler"
version: "0.5.1+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/unicycler_scrub"
---

# unicycler\_scrub(1)

read trimming, chimera detection and misassembly detection

## NAME

unicycler\_scrub - read trimming, chimera detection and misassembly detection

## SYNOPSIS

**unicycler\_scrub** \[-h\] **-i** INPUT **-o** OUT \[-r READS\] \[--trim TRIM\] \[--split SPLIT\] \[--min\_split\_size MIN\_SPLIT\_SIZE\] \[--discard\_chimeras\] \[-t THREADS\] \[--keep\_paf\] \[--parameters PARAMETERS\] \[--verbosity VERBOSITY\]

## DESCRIPTION

Unicycler-scrub - read trimming, chimera detection and misassembly detection

## OPTIONS

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

  show this help message and exit

- **-i** INPUT, **--input** INPUT

  These are the reads or assembly to be scrubbed (can be FASTA or FASTQ format

- **-o** OUT, **--out** OUT

  The scrubbed reads or assembly will be saved to this file (will have the same format as the **--input** file format) or use "none" to not produce an output file

- **-r** READS, **--reads** READS

  These are the reads used to scrub **--input** (can be FASTA or FASTQ format) (default: same file as **--input**)

- **--trim** TRIM

  The aggressiveness with which the input will be trimmed (0 to 100, where 0 is no trimming and 100 is very aggressive trimming) (default: 50)

- **--split** SPLIT

  The aggressiveness with which the input will be split (0 to 100, where 0 is no splitting and 100 is very aggressive splitting) (default: 50)

- **--min\_split\_size** MIN\_SPLIT\_SIZE

  Parts of split sequences will only be outputted if they are at least this big (default: 1000)

- **--discard\_chimeras**

  If used, chimeric sequences will be discarded instead of split (default: False)

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

  Number of threads used (default: 4)

- **--keep\_paf**

  Save the alignments to file (makes repeated runs faster because alignments can be loaded from file) (default: False)

- **--parameters** PARAMETERS

  Low-level parameters (for debugging use only) (default: )

- **--verbosity** VERBOSITY

  Level of stdout information (default: 1)

-

  0 = no stdout,

-

  1 = basic progress indicators,

-

  2 = extra info,

-

  3 = debugging info

## SEE ALSO

[unicycler(1)](/unicycler/1.md)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.