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A package for handling whole genome alignments by Pádraic Corcoran and Henry Barton

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WGAbed - a package for handling whole genome alignments

About

This packages handles the conversion of a whole genome alignment file in MAF format to a reference ordered BED format containing all the information in the MAF file but in a more accessible format. This repository contains scripts for creating a 'whole genome alignment BED' or 'WGAbed' file as well as scripts for downstream manipulation of the file.

The package was conceived and implemented by Pádraic Corcoran (https://github.com/padraicc), with additions and later implemented scripts by Henry Barton (https://github.com/henryjuho).

Documentation

Documentation for the package can be found at: https://henryjuho.github.io/WGAbed.

Running

The package requires the pysam module: http://pysam.readthedocs.io/en/latest/index.html.

To obtain the package code issue:

git clone https://github.com/henryjuho/WGAbed.git

About

A package for handling whole genome alignments by Pádraic Corcoran and Henry Barton

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