The Bacterial and Archaeal Genome Analyser (BAGA, pronounced "baga") is a commandline application and Python 2 package (3 coming soon) for diverse analyses of genome sequence data designed to facilitate reproducible research.
Input data can be complete genome sequences and/or paired end short reads from Illumina sequencers, typically whole genome shotgun libraries. Tasks might include variant calling and resolving population structure of resequenced pathogen isolates, analysis of evolution experiments and comparative genomics including phylogenomics. Click here to go straight to the documentation.
BAGA is a wrapper for proven third party tools1, but also includes novel algorithms for identifying chromosomal rearrangements and sequence repeats known to increase the likelihood of false positive variant calls2, the means to filter those probable false positive variants out of a dataset, the means to create custom pipelines for reproducible analyses3, and can generate various informative plots4. It is under active development: new features and much more documentation will be appearing shortly.
Please see the documentation for more details and step by step guides for performing various analysis pipelines and making your research more easily reproducible.
Work on this software was started at The University of Liverpool, UK with funding from The Wellcome Trust (093306/Z/10) awarded to:
License GPLv3+: GNU GPL version 3 or later. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.