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)

AUTHOR

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