README.md

Bio-PacbioMethylation

Runs Pacbio methylation pipeline

This repository is no longer supported. Use at your own risk.

Contents

• Introduction
• Installation
  • Required dependencies
  • From Source
  • Running the tests
• Usage
• License
• Feedback/Issues

Introduction

Runs the RS_Modification_and_Motif_Analysis pipeline and tidies output files.

Installation

Bio-PacbioMethylation has the following dependencies:

Required dependencies

• tabix
• bgzip

Details for installing Bio-PacbioMethylation are provided below. If you encounter an issue when installing Bio-PacbioMethylation please contact your local system administrator. If you encounter a bug please log it here or email us at [email protected].

From Source

Clone the repository:

git clone https://github.com/sanger-pathogens/Bio-PacbioMethylation.git

Move into the directory and install all dependencies using DistZilla:

cd Bio-PacbioMethylation
dzil authordeps --missing | cpanm
dzil listdeps --missing | cpanm

Run the tests:

dzil test
If the tests pass, install Bio-PacbioMethylation:

dzil install

Running the tests

The test can be run with dzil from the top level directory:

dzil test

Usage

pacbio_methylation [options] <output dir> <reference.fasta> <*.bax.h5>

Runs the Pacio Methylation pipeline, makes Artemis plot files, and
cleans up unneeded files.

Options:

-h,help
    Show this help and exit

-m,-min_ipdratio
    Cutoff for the ipdratio when making Artemis plot file.
    Any value less than -min_ipdratio will be set to zero [0]

-n,-noclean
    Do not delete intermediate files

-t,-threads INT
    Number of threads [1]

License

Bio-PacbioMethylation is free software, licensed under GPLv3.