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

# unicycler(1)

assembly pipeline for bacterial genomes

## NAME

unicycler - assembly pipeline for bacterial genomes

## SYNOPSIS

**unicycler** \[-h\] \[--help\_all\] \[--version\] \[-1 SHORT1\] \[-2 SHORT2\] \[-s UNPAIRED\] \[-l LONG\] **-o** OUT \[--verbosity VERBOSITY\] \[--min\_fasta\_length MIN\_FASTA\_LENGTH\] \[--keep KEEP\] \[-t THREADS\] \[--mode {conservative,normal,bold}\] \[--linear\_seqs LINEAR\_SEQS\] \[--vcf\]

## DESCRIPTION

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.

## OPTIONS

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

  Show this help message and exit

- **--help\_all**

  Show a help message with all program options

- **--version**

  Show Unicycler's version number

### Input

- **-1** SHORT1, **--short1** SHORT1

  FASTQ file of first short reads in each pair (required)

- **-2** SHORT2, **--short2** SHORT2

  FASTQ file of second short reads in each pair (required)

- **-s** UNPAIRED, **--unpaired** UNPAIRED

  FASTQ file of unpaired short reads (optional)

- **-l** LONG, **--long** LONG

  FASTQ or FASTA file of long reads (optional)

### Output

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

  Output directory (required)

- **--verbosity** VERBOSITY

  Level of stdout and log file information (default: 1)

-

  0 = no stdout,

-

  1 = basic progress indicators,

-

  2 = extra info,

-

  3 = debugging info

- **--min\_fasta\_length** MIN\_FASTA\_LENGTH

  Exclude contigs from the FASTA file which are shorter than this length (default: 100)

- **--keep** KEEP

  Level of file retention (default: 1)

-

  0 = only keep final files: assembly (FASTA,GFA and log),

-

  1 = also save graphs at main checkpoints,

-

  2 = also keep SAM (enables fast rerun in different mode),

-

  3 = keep all temp files and save all graphs (for debugging)

- **--vcf**

  Produce a VCF by mapping the short reads to the final assembly (experimental, default: do not produce a vcf file)

### Other

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

  Number of threads used (default: 4)

- **--mode** {conservative,normal,bold}

  Bridging mode (default: normal)

-

  conservative = smaller contigs, lowest misassembly rate

-

  normal = moderate contig size and misassembly rate

-

  bold = longest contigs, higher misassembly rate

- **--linear\_seqs** LINEAR\_SEQS

  The expected number of linear (i.e. non-circular) sequences in the underlying sequence (default: 0)

## AUTHOR

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