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)