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###MGA: Multi-genome alignment contaminant screen for high-throughput sequence data

MGA is a quality control tool for high-throughput sequence data. It screens for contaminants by aligning sequence reads in FASTQ format against a series of reference genomes using Bowtie and against a set of adapter sequences using exonerate.

MGA samples a subset of the reads, by default 100000, prior to alignment against reference genome sequences and adapters. This reduces considerably the overall run time. In addition, the reads are trimmed to 36 bases by default, prior to alignment by Bowtie. This is to ensure consistency of the output mapping and error rates across runs of differing lengths. Exonerate alignment against adapters uses the full-length sequences.

####Installing and running MGA

Please see README file for details of how to install and run MGA from a pre-packaged release.

####Building MGA from source

MGA is built using Apache Maven, a software project management and build automation tool. Details on how to install and run Maven can be found here.

Maven will automatically download dependencies from the central Maven repository and a repository hosted by Cancer Research UK Cambridge Institute (CRUK-CI). The latter contains the Java libraries and source code for the workflow system that MGA depends on, which is also developed at CRUK-CI.

1. Clone the MGA project

    git clone https://github.com/crukci-bioinformatics/MGA.git
   

2. Build and package MGA

    cd MGA
    mvn package
   

3. Unpack MGA to installation directory (substituting for the version number as appropriate)

    tar zxf target/mga-1.x-distribution.tar.gz
   

This will create a directory named mga-1.x which can be moved to the desired installation directory.