.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH PILON "1" "June 2018" "pilon 1.22" "User Commands"
.SH NAME
pilon \- automated genome assembly improvement and variant detection tool
.SH SYNOPSIS
.B pilon
\fB\-\-genome\fR genome.fasta [\-\-frags frags.bam] [\-\-jumps jumps.bam] [\-\-unpaired unpaired.bam]
[...other options...]
.SH DESCRIPTION
Pilon is a software tool which can be used to:
.IP \[bu] 2
Automatically improve draft assemblies
.IP \[bu]
Find variation among strains, including large event detection
.P
Pilon requires as input a FASTA file of the genome along with one or more
BAM files of reads aligned to the input FASTA file. Pilon uses read
alignment analysis to identify inconsistencies between the input genome and
the evidence in the reads. It then attempts to make improvements to the
input genome, including:
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Single base differences
.IP \[bu]
Small indels
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Larger indel or block substitution events
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Gap filling
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Identification of local misassemblies, including optional opening of new gaps
.SH OPTIONS
.TP
\fB\-\-help\fR
.IP
for option details
.SS INPUTS
.IP
\fB\-\-genome\fR genome.fasta
.IP
The input genome we are trying to improve, which must be the reference used
for the bam alignments.  At least one of \fB\-\-frags\fR or \fB\-\-jumps\fR must also be given.
.IP
\fB\-\-frags\fR frags.bam
.IP
A bam file consisting of fragment paired\-end alignments, aligned to the \fB\-\-genome\fR
argument using bwa or bowtie2.  This argument may be specified more than once.
.IP
\fB\-\-jumps\fR jumps.bam
.IP
A bam file consisting of jump (mate pair) paired\-end alignments, aligned to the
\fB\-\-genome\fR argument using bwa or bowtie2.  This argument may be specified more than once.
.IP
\fB\-\-unpaired\fR unpaired.bam
.IP
A bam file consisting of unpaired alignments, aligned to the \fB\-\-genome\fR argument
using bwa or bowtie2.  This argument may be specified more than once.
.IP
\fB\-\-bam\fR any.bam
.IP
A bam file of unknown type; Pilon will scan it and attempt to classify it as one
of the above bam types.
.SS OUTPUTS
.IP
\fB\-\-output\fR prefix
.IP
Prefix for output files
.IP
\fB\-\-outdir\fR directory
.IP
Use this directory for all output files.
.IP
\fB\-\-changes\fR
.IP
If specified, a file listing changes in the <output>.fasta will be generated.
.IP
\fB\-\-vcf\fR
.IP
If specified, a vcf file will be generated
.IP
\fB\-\-vcfqe\fR
.IP
If specified, the VCF will contain a QE (quality\-weighted evidence) field rather
than the default QP (quality\-weighted percentage of evidence) field.
.IP
\fB\-\-tracks\fR
.IP
This options will cause many track files (*.bed, *.wig) suitable for viewing in
a genome browser to be written.
.SS CONTROL
.IP
\fB\-\-variant\fR
.IP
Sets up heuristics for variant calling, as opposed to assembly improvement;
equivalent to "\-\-vcf \fB\-\-fix\fR all,breaks".
.IP
\fB\-\-chunksize\fR
.IP
Input FASTA elements larger than this will be processed in smaller pieces not to
exceed this size (default 10000000).
.IP
\fB\-\-diploid\fR
.IP
Sample is from diploid organism; will eventually affect calling of heterozygous SNPs
.IP
\fB\-\-fix\fR fixlist
.IP
A comma\-separated list of categories of issues to try to fix:
.IP
"snps": try to fix individual base errors;
"indels": try to fix small indels;
"gaps": try to fill gaps;
"local": try to detect and fix local misassemblies;
"all": all of the above (default);
"bases": shorthand for "snps" and "indels" (for back compatibility);
"none": none of the above; new fasta file will not be written.
.IP
The following are experimental fix types:
.IP
"amb": fix ambiguous bases in fasta output (to most likely alternative);
"breaks": allow local reassembly to open new gaps (with "local");
"circles": try to close circlar elements when used with long corrected reads;
"novel": assemble novel sequence from unaligned non\-jump reads.
.IP
\fB\-\-dumpreads\fR
.IP
Dump reads for local re\-assemblies.
.IP
\fB\-\-duplicates\fR
.IP
Use reads marked as duplicates in the input BAMs (ignored by default).
.IP
\fB\-\-iupac\fR
.IP
Output IUPAC ambiguous base codes in the output FASTA file when appropriate.
.IP
\fB\-\-nonpf\fR
.IP
Use reads which failed sequencer quality filtering (ignored by default).
.IP
\fB\-\-targets\fR targetlist
.IP
Only process the specified target(s).
Targets are comma\-separated, and each target
.IP
is a fasta element name optionally followed by a base range.
Example: "scaffold00001,scaffold00002:10000\-20000" would result in processing all of
scaffold00001 and coordinates 10000\-20000 of scaffold00002.
If "targetlist" is the name of a file, each line will be treated as a target
specification.
.IP
\fB\-\-threads\fR
.IP
Degree of parallelism to use for certain processing (default 1). Experimental.
.IP
\fB\-\-verbose\fR
.IP
More verbose output.
.IP
\fB\-\-debug\fR
.IP
Debugging output (implies verbose).
.IP
\fB\-\-version\fR
.IP
Print version string and exit.
.SS HEURISTICS:
.IP
\fB\-\-defaultqual\fR qual
.IP
Assumes bases are of this quality if quals are no present in input BAMs (default 15).
.IP
\fB\-\-flank\fR nbases
.IP
Controls how much of the well\-aligned reads will be used; this many bases at each
end of the good reads will be ignored (default 10).
.IP
\fB\-\-gapmargin\fR
.IP
Closed gaps must be within this number of bases of true size to be closed (100000)
.IP
\fB\-\-K\fR
.IP
Kmer size used by internal assembler (default 47).
.IP
\fB\-\-mindepth\fR depth
.IP
Variants (snps and indels) will only be called if there is coverage of good pairs
at this depth or more; if this value is >= 1, it is an absolute depth, if it is a
fraction < 1, then minimum depth is computed by multiplying this value by the mean
coverage for the region, with a minimum value of 5 (default 0.1: min depth to call
is 10% of mean coverage or 5, whichever is greater).
.IP
\fB\-\-mingap\fR
.IP
Minimum size for unclosed gaps (default 10)
.IP
\fB\-\-minmq\fR
.IP
Minimum alignment mapping quality for a read to count in pileups (default 0)
.IP
\fB\-\-minqual\fR
.IP
Minimum base quality to consider for pileups (default 0)
.IP
\fB\-\-nostrays\fR
.IP
Skip making a pass through the input BAM files to identify stray pairs, that is,
those pairs in which both reads are aligned but not marked valid because they have
inconsistent orientation or separation. Identifying stray pairs can help fill gaps
and assemble larger insertions, especially of repeat content.  However, doing so
sometimes consumes considerable memory.
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.