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Pipeline to identify intron insertions/deletions
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COPYING
IntronPoly.pm
README.md
arguments.md
find_distrib.pl
find_types.pl
infer_fraglen.pl
intron_poly.xml
ip_handler.pl
rerun.pl
sam2fasta.pl
sam2fastq.pl
sam2pefastq.pl
sam2raw.pl
simulate.pl
trim2.pl
trim_fasta.pl
trim_fastq.pl
validate_fasta.pl
validate_fastq.pl

README.md

intron-polymorphism


Discovers intron insertions and deletions from samples of closely related organisms.

EXTERNAL DEPENDENCIES

The following packages must be installed and added to your PATH:

  1. BWA

  2. Blast

  3. ClustalW

  4. Taipan

INSTALLATION

Linux (64-bit)

Install required Perl module:

sudo cpan IPC::System::Simple

Install project code:

git clone git://github.com/rmtheis/intron-polymorphism.git

RUNNING

cd intron-polymorphism
perl ip_handler.pl --ref-genome genome.fa -1 myfile_1.fq -2 myfile_2.fq --trim-reads

PARAMETERS

See arguments.md for a description of the command line parameters.

Usage:
    ip_handler.pl [required arguments] [options]

Required Arguments:
    -g/--ref-genome              <string>
    -1/--mate1-file              <string>
    -2/--mate2-file              <string>

Options:
    -o/--output-dir               <string>     [ default: ip_out    ]
    -f/--fragment-length          <int>        [ default: detect    ]
    -a/--min-mates                <int>        [ default: 3         ]
    -l/--min-contig-length        <int>        [ default: 70        ]
    -m/--max-intron-length        <int>        [ default: 250       ]
    -t/--tolerance-simpair        <int>        [ default: 10        ]
    -r/--tolerance-blast          <int>        [ default: 500       ]
    --trim-reads
    --validate-reads
    --version

LICENSE

Apache License, Version 2.0

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