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

# unicycler\_polish(1)

Unicycler polish - hybrid assembly polishing

## NAME

unicycler\_polish - Unicycler polish - hybrid assembly polishing

## SYNOPSIS

**unicycler\_polish** \[-h\] **-a** ASSEMBLY \[-1 SHORT1\] \[-2 SHORT2\] \[--pb\_bax PB\_BAX \[PB\_BAX ...\]\] \[--pb\_bam PB\_BAM\] \[--pb\_fasta PB\_FASTA\] \[--long\_reads LONG\_READS\] \[--no\_fix\_local\] \[--min\_insert MIN\_INSERT\] \[--max\_insert MAX\_INSERT\] \[--min\_align\_length MIN\_ALIGN\_LENGTH\] \[--homopolymer HOMOPOLYMER\] \[--large LARGE\] \[--illumina\_alt ILLUMINA\_ALT\] \[--freebayes\_qual\_cutoff FREEBAYES\_QUAL\_CUTOFF\] \[--threads THREADS\] \[--verbosity VERBOSITY\] \[--samtools SAMTOOLS\] \[--bowtie2 BOWTIE2\] \[--minimap2 MINIMAP2\] \[--freebayes FREEBAYES\] \[--pitchfork PITCHFORK\] \[--bax2bam BAX2BAM\] \[--pbalign PBALIGN\] \[--arrow ARROW\] \[--pilon PILON\] \[--java JAVA\] \[--ale ALE\] \[--racon RACON\] \[--minimap MINIMAP\] \[--nucmer NUCMER\] \[--showsnps SHOWSNPS\]

## DESCRIPTION

Unicycler polish - hybrid assembly polishing

## OPTIONS

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

  show this help message and exit

### Assembly

- **-a** ASSEMBLY, **--assembly** ASSEMBLY

  Input assembly to be polished

### Short reads

-

  To polish with short reads (using Pilon), provide two FASTQ files of paired-end reads

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

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

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

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

### PacBio reads

-

  To polish with PacBio reads (using Arrow), provide one of the following

- **--pb\_bax** PB\_BAX \[PB\_BAX ...\]

  PacBio raw bax.h5 read files

- **--pb\_bam** PB\_BAM

  PacBio BAM read file

- **--pb\_fasta** PB\_FASTA

  FASTA file of PacBio reads

### Generic long reads

-

  To polish with generic long reads, provide the following

- **--long\_reads** LONG\_READS

  FASTQ/FASTA file of long reads

### Polishing settings

Various settings for polishing behaviour (defaults should work well in most cases)

- **--no\_fix\_local**

  do not fix local misassemblies (default: False)

- **--min\_insert** MIN\_INSERT

  minimum valid short read insert size (default: auto)

- **--max\_insert** MAX\_INSERT

  maximum valid short read insert size (default: auto)

- **--min\_align\_length** MIN\_ALIGN\_LENGTH

  Minimum long read alignment length (default: 1000)

- **--homopolymer** HOMOPOLYMER

  Long read polish changes to a homopolymer of this length or greater will be ignored (default: 4)

- **--large** LARGE

  Variants of this size or greater will be assess as large variants (default: 10)

- **--illumina\_alt** ILLUMINA\_ALT

  When assessing long read changes with short read alignments, a variant will only be applied if the alternative occurrences in the short read alignments exceed this percentage (default: 5)

- **--freebayes\_qual\_cutoff** FREEBAYES\_QUAL\_CUTOFF

  Reject Pilon substitutions from long reads if the FreeBayes quality is less than this value (default: 10.0)

### Other settings

- **--threads** THREADS

  CPU threads to use in alignment and consensus (default: number of CPUs)

- **--verbosity** VERBOSITY

  Level of stdout information (0 to 3, default: 2) 0 = no stdout, 1 = basic progress indicators, 2 = extra info, 3 = debugging info

### Tool locations

If these required tools are not available in your PATH variable, specify their location here (depending on which input reads are used, some of these tools may not be required)

- **--samtools** SAMTOOLS

  path to samtools executable (default: samtools)

- **--bowtie2** BOWTIE2

  path to bowtie2 executable (default: bowtie2)

- **--minimap2** MINIMAP2

  path to minimap2 executable (default: minimap2)

- **--freebayes** FREEBAYES

  path to freebayes executable (default: freebayes)

- **--pitchfork** PITCHFORK

  Path to Pitchfork installation of PacBio tools (should contain bin and lib directories) (default: )

- **--bax2bam** BAX2BAM

  path to bax2bam executable (default: bax2bam)

- **--pbalign** PBALIGN

  path to pbalign executable (default: pbalign)

- **--arrow** ARROW

  path to arrow executable (default: arrow)

- **--pilon** PILON

  path to pilon jar file (default: pilon\*.jar)

- **--java** JAVA

  path to java executable (default: java)

- **--ale** ALE

  path to ALE executable (default: ALE)

- **--racon** RACON

  path to racon executable (default: racon)

- **--minimap** MINIMAP

  path to miniasm executable (default: minimap)

- **--nucmer** NUCMER

  path to nucmer executable (default: nucmer)

- **--showsnps** SHOWSNPS

  path to show-snps executable (default: show-snps)

## 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.