Pilon-Teaching

Category

Bioinformatics

Program On

Teaching

Version

1.22

Author / Distributor

pilon

Description

"Pilon is a software tool which can be used to: (i) Automatically improve draft assemblies, (ii)Find variation among strains, including large event detection" More details are at pilon

Running Program

The last version of this application is at /usr/local/apps/eb/pilon/1.22-Java-1.8.0_144

To use this version, please load the module with

ml pilon/1.22-Java-1.8.0_144 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_pilon
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=pilon.%j.out
#SBATCH --error=pilon.%j.err

cd $SLURM_SUBMIT_DIR
ml pilon/1.22-Java-1.8.0_144
java -jar /usr/local/apps/eb/pilon/1.22-Java-1.8.0_144/pilon-1.22.jar [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml pilon/1.22-Java-1.8.0_144 
java -jar /usr/local/apps/eb/pilon/1.22-Java-1.8.0_144/pilon-1.22.jar --help
Pilon version 1.22 Wed Mar 15 16:38:30 2017 -0400

    Usage: pilon --genome genome.fasta [--frags frags.bam] [--jumps jumps.bam] [--unpaired unpaired.bam]
                 [...other options...]
           pilon --help for option details 


         INPUTS:
           --genome genome.fasta
              The input genome we are trying to improve, which must be the reference used
              for the bam alignments.  At least one of --frags or --jumps must also be given.
           --frags frags.bam
              A bam file consisting of fragment paired-end alignments, aligned to the --genome
              argument using bwa or bowtie2.  This argument may be specifed more than once.
           --jumps jumps.bam
              A bam file consisting of jump (mate pair) paired-end alignments, aligned to the
              --genome argument using bwa or bowtie2.  This argument may be specifed more than once.
           --unpaired unpaired.bam
              A bam file consisting of unpaired alignments, aligned to the --genome argument 
              using bwa or bowtie2.  This argument may be specifed more than once.
           --bam any.bam
              A bam file of unknown type; Pilon will scan it and attempt to classify it as one
              of the above bam types.
         OUTPUTS:
           --output prefix
              Prefix for output files
           --outdir directory
              Use this directory for all output files.
           --changes
              If specified, a file listing changes in the <output>.fasta will be generated.
           --vcf
              If specified, a vcf file will be generated
           --vcfqe
               If specified, the VCF will contain a QE (quality-weighted evidence) field rather
               than the default QP (quality-weighted percentage of evidence) field.
           --tracks
               This options will cause many track files (*.bed, *.wig) suitable for viewing in
               a genome browser to be written.
         CONTROL:
           --variant
              Sets up heuristics for variant calling, as opposed to assembly improvement;
              equivalent to "--vcf --fix all,breaks".
           --chunksize
              Input FASTA elements larger than this will be processed in smaller pieces not to
              exceed this size (default 10000000).
           --diploid
              Sample is from diploid organism; will eventually affect calling of heterozygous SNPs
           --fix fixlist
              A comma-separated list of categories of issues to try to fix:
                "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.
              The following are experimental fix types:
                "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.
           --dumpreads
              Dump reads for local re-assemblies.
           --duplicates
              Use reads marked as duplicates in the input BAMs (ignored by default).
           --iupac
              Output IUPAC ambiguous base codes in the output FASTA file when appropriate.
           --nonpf
              Use reads which failed sequencer quality filtering (ignored by default).
           --targets targetlist
              Only process the specified target(s).  Targets are comma-separated, and each target
              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.
           --threads
              Degree of parallelism to use for certain processing (default 1). Experimental.
           --verbose
              More verbose output.
           --debug
              Debugging output (implies verbose).
           --version
              Print version string and exit.
         HEURISTICS:
           --defaultqual qual
              Assumes bases are of this quality if quals are no present in input BAMs (default 15).
           --flank nbases
              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).
           --gapmargin
              Closed gaps must be within this number of bases of true size to be closed (100000)
           --K
              Kmer size used by internal assembler (default 47).
           --mindepth depth
              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 minumum value of 5 (default 0.1: min depth to call 
              is 10% of mean coverage or 5, whichever is greater).
           --mingap
              Minimum size for unclosed gaps (default 10)
           --minmq
              Minimum alignment mapping quality for a read to count in pileups (default 0)
           --minqual
              Minimum base quality to consider for pileups (default 0)
           --nostrays
              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.

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Installation

Source code is obtained from pilon

System

64-bit Linux