unicycler_polish - Unicycler polish - hybrid assembly polishing

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

unicycler_polish 0.4.7                            October 2018                               UNICYCLER_POLISH(1)

       Unicycler polish - hybrid assembly polishing

       unicycler_polish - Unicycler polish - hybrid assembly polishing

-h, --help
              show this help message and exit

   Assembly-a ASSEMBLY, --assembly ASSEMBLY
              Input assembly to be polished

   Shortreads
              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)

   PacBioreads
              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

   Genericlongreads
              To polish with generic long reads, provide the following

       --long_reads LONG_READS
              FASTQ/FASTA file of long reads

   Polishingsettings
       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)

   Othersettings--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

   Toollocations
       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)

unicycler(1)

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]