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

# unicycler\_align(1)

sensitive semi-global long read aligner

## NAME

unicycler\_align - sensitive semi-global long read aligner

## SYNOPSIS

**unicycler\_align** \[-h\] **--ref** REF **--reads** READS **--sam** SAM \[--contamination CONTAMINATION\] \[--scores SCORES\] \[--low\_score LOW\_SCORE\] \[--keep\_bad\] \[--sensitivity SENSITIVITY\] \[--threads THREADS\] \[--verbosity VERBOSITY\] \[--min\_len MIN\_LEN\] \[--allowed\_overlap ALLOWED\_OVERLAP\]

## DESCRIPTION

Unicycler align - a sensitive semi-global long read aligner

## OPTIONS

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

  show this help message and exit

- **--ref** REF

  FASTA file containing one or more reference sequences

- **--reads** READS

  FASTQ or FASTA file of long reads

- **--sam** SAM

  SAM file of resulting alignments

- **--contamination** CONTAMINATION

  FASTA file of known contamination in long reads

- **--scores** SCORES

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

- **--low\_score** LOW\_SCORE

  Score threshold - alignments below this are considered poor (default: set threshold automatically)

- **--keep\_bad**

  Include alignments in the results even if they are below the low score threshold (default: low-scoring alignments are discarded)

- **--sensitivity** SENSITIVITY

  A number from 0 (least sensitive) to 3 (most sensitive) (default: 0)

- **--threads** THREADS

  Number of threads used (default: number of CPUs, up to 8)

- **--verbosity** VERBOSITY

  Level of stdout information (0 to 4) (default: 1)

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

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

- **--allowed\_overlap** ALLOWED\_OVERLAP

  Allow this much overlap between alignments in a single read (default: 100)

## 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.