.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH UNICYCLER_POLISH "1" "October 2018" "unicycler_polish 0.4.7" "User Commands"
.SH NAME
unicycler_polish \- Unicycler polish - hybrid assembly polishing
.SH SYNOPSIS
.B unicycler_polish
[\-h] \fB\-a\fR 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]
.SH DESCRIPTION
Unicycler polish \- hybrid assembly polishing
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS Assembly
.TP
\fB\-a\fR ASSEMBLY, \fB\-\-assembly\fR ASSEMBLY
Input assembly to be polished
.SS Short reads
.IP
To polish with short reads (using Pilon), provide two FASTQ files of
paired\-end reads
.TP
\fB\-1\fR SHORT1, \fB\-\-short1\fR SHORT1
FASTQ file of short reads (first reads in each pair)
.TP
\fB\-2\fR SHORT2, \fB\-\-short2\fR SHORT2
FASTQ file of short reads (second reads in each
pair)
.SS PacBio reads
.IP
To polish with PacBio reads (using Arrow), provide one of the following
.TP
\fB\-\-pb_bax\fR PB_BAX [PB_BAX ...]
PacBio raw bax.h5 read files
.TP
\fB\-\-pb_bam\fR PB_BAM
PacBio BAM read file
.TP
\fB\-\-pb_fasta\fR PB_FASTA
FASTA file of PacBio reads
.SS Generic long reads
.IP
To polish with generic long reads, provide the following
.TP
\fB\-\-long_reads\fR LONG_READS
FASTQ/FASTA file of long reads
.SS Polishing settings
Various settings for polishing behaviour (defaults should work well in
most cases)
.TP
\fB\-\-no_fix_local\fR
do not fix local misassemblies (default: False)
.TP
\fB\-\-min_insert\fR MIN_INSERT
minimum valid short read insert size (default: auto)
.TP
\fB\-\-max_insert\fR MAX_INSERT
maximum valid short read insert size (default: auto)
.TP
\fB\-\-min_align_length\fR MIN_ALIGN_LENGTH
Minimum long read alignment length (default: 1000)
.TP
\fB\-\-homopolymer\fR HOMOPOLYMER
Long read polish changes to a homopolymer of this
length or greater will be ignored (default: 4)
.TP
\fB\-\-large\fR LARGE
Variants of this size or greater will be assess as
large variants (default: 10)
.TP
\fB\-\-illumina_alt\fR 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)
.TP
\fB\-\-freebayes_qual_cutoff\fR FREEBAYES_QUAL_CUTOFF
Reject Pilon substitutions from long reads if the
FreeBayes quality is less than this value (default:
10.0)
.SS Other settings
.TP
\fB\-\-threads\fR THREADS
CPU threads to use in alignment and consensus
(default: number of CPUs)
.TP
\fB\-\-verbosity\fR VERBOSITY
Level of stdout information (0 to 3, default: 2)
0 = no stdout, 1 = basic progress indicators,
2 = extra info, 3 = debugging info
.SS 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)
.TP
\fB\-\-samtools\fR SAMTOOLS
path to samtools executable (default: samtools)
.TP
\fB\-\-bowtie2\fR BOWTIE2
path to bowtie2 executable (default: bowtie2)
.TP
\fB\-\-minimap2\fR MINIMAP2
path to minimap2 executable (default: minimap2)
.TP
\fB\-\-freebayes\fR FREEBAYES
path to freebayes executable (default: freebayes)
.TP
\fB\-\-pitchfork\fR PITCHFORK
Path to Pitchfork installation of PacBio tools
(should contain bin and lib directories) (default: )
.TP
\fB\-\-bax2bam\fR BAX2BAM
path to bax2bam executable (default: bax2bam)
.TP
\fB\-\-pbalign\fR PBALIGN
path to pbalign executable (default: pbalign)
.TP
\fB\-\-arrow\fR ARROW
path to arrow executable (default: arrow)
.TP
\fB\-\-pilon\fR PILON
path to pilon jar file (default: pilon*.jar)
.TP
\fB\-\-java\fR JAVA
path to java executable (default: java)
.TP
\fB\-\-ale\fR ALE
path to ALE executable (default: ALE)
.TP
\fB\-\-racon\fR RACON
path to racon executable (default: racon)
.TP
\fB\-\-minimap\fR MINIMAP
path to miniasm executable (default: minimap)
.TP
\fB\-\-nucmer\fR NUCMER
path to nucmer executable (default: nucmer)
.TP
\fB\-\-showsnps\fR SHOWSNPS
path to show\-snps executable (default: show\-snps)
.SH SEE ALSO
unicycler(1)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.