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

# unicycler\_check(1)

long read assembly checker

## NAME

unicycler\_check - long read assembly checker

## SYNOPSIS

**unicycler\_check** \[-h\] **--sam** SAM **--ref** REF **--reads** READS \[--min\_len MIN\_LEN\] \[--error\_window\_size ERROR\_WINDOW\_SIZE\] \[--depth\_window\_size DEPTH\_WINDOW\_SIZE\] \[--error\_rate\_threshold ERROR\_RATE\_THRESHOLD\] \[--depth\_p\_val DEPTH\_P\_VAL\] \[--window\_tables WINDOW\_TABLES\] \[--base\_tables BASE\_TABLES\] \[--html HTML\] \[--threads THREADS\] \[--verbosity VERBOSITY\]

## DESCRIPTION

Long read assembly checker

## OPTIONS

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

  show this help message and exit

- **--sam** SAM

  Input SAM file of alignments (if this file doesn't exist, the alignment will be performed with results saved to this file - you can use the aligner arguments with this script)

- **--ref** REF

  FASTA file containing one or more reference sequences

- **--reads** READS

  FASTQ file of long reads

- **--min\_len** MIN\_LEN

  Minimum alignment length (bp) - exclude alignments shorter than this length (default: 100)

- **--error\_window\_size** ERROR\_WINDOW\_SIZE

  Window size for error summaries (default: 100)

- **--depth\_window\_size** DEPTH\_WINDOW\_SIZE

  Window size for depth summaries (default: 100)

- **--error\_rate\_threshold** ERROR\_RATE\_THRESHOLD

  Threshold for high error rates, expressed as the fraction between the mean error rate and the random alignment error rate (default: 0.3)

- **--depth\_p\_val** DEPTH\_P\_VAL

  P-value for low/high depth thresholds (default: 0.001)

- **--window\_tables** WINDOW\_TABLES

  Path and/or prefix for table files summarising reference errors for reference windows (default: do not save window tables)

- **--base\_tables** BASE\_TABLES

  Path and/or prefix for table files summarising reference errors at each base (default: do not save base tables)

- **--html** HTML

  Path for HTML report (default: do not save HTML report)

- **--threads** THREADS

  Number of CPU threads used to align (default: the number of available CPUs)

- **--verbosity** VERBOSITY

  Level of stdout information (0 to 2) (default: 1)

## 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.