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baga

Bacterial and Archaeal Genome Analyser

https://github.com/daveuu/baga

Science Score: 18.0%

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Repository

Bacterial and Archaeal Genome Analyser

Basic Info
  • Host: GitHub
  • Owner: daveuu
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Size: 914 KB
Statistics
  • Stars: 9
  • Watchers: 3
  • Forks: 2
  • Open Issues: 11
  • Releases: 0
Created almost 11 years ago · Last pushed over 8 years ago
Metadata Files
Readme License Citation

README.md

Bacterial and Archaeal Genome Analyser

Novel analyses and wrapped tools pipelined for convenient processing of genome sequences

David Williams

Introduction

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.

  1. e.g. BWA for short read alignment to longer sequences, GATK for variant calling and ClonalFrameML for homologous recombination inference
  2. Variant calls in such regions are unreliable and should be filtered because conventional variant calling algorithms would be unaware of potential misalignments caused by the loss of homology and might therefore report false positive variant calls e.g., near chromosomal rearrangements caused by mobile genetic elements. Detailed characterisation of those regions can be made by local de novo assemblies of reads and alignment of resulting contigs to the reference sequence
  3. researchers can make use of version-control and digital object identifiers to generate citable and reproducible analyses for peer review publication
  4. BAGA can plot all automatically indicated regions such as those prone to misalignment of short reads because of structural differences between a reference sequence and a sampled genome, e.g. a missing prophage (see point 2 above)

Please see the documentation for more details and step by step guides for performing various analysis pipelines and making your research more easily reproducible.

Funding

Work on this software was started at The University of Liverpool, UK with funding from The Wellcome Trust (093306/Z/10) awarded to:

  • Dr Steve Paterson (The University of Liverpool, UK)
  • Dr Craig Winstanley (The University of Liverpool, UK)
  • Dr Michael A Brockhurst (The University of York, UK)

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.

Owner

  • Name: David Williams
  • Login: daveuu
  • Kind: user
  • Location: London, UK

Citation (citations.bib) 

% This file was created with JabRef 2.10.
% Encoding: UTF8


@Article{spades,
  Title                    = {SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing},
  Author                   = {Bankevich, A. and Nurk, S. and Antipov, D. and Gurevich, A. A. and Dvorkin, M. and Kulikov, A. S. and Lesin, V. M. and Nikolenko, S. I. and Pham, S. and Prjibelski, A. D. and Pyshkin, A. V. and Sirotkin, A. V. and Vyahhi, N. and Tesler, G. and Alekseyev, M. A. and Pevzner, P. A.},
  Journal                  = {J. Comput. Biol.},
  Year                     = {2012},
  Number                   = {5},
  Pages                    = {455--477},
  Volume                   = {19}
}

@Article{biopython,
  Title                    = {Biopython: Freely available Python tools for computational molecular biology and bioinformatics},
  Author                   = {Cock, P.J.A. and Antao, T. and Chang, J.T. and Chapman, B.A. and Cox, C.J. and Dalke, A. and Friedberg, I. and Hamelryck, T. and Kauff, F. and Wilczynski, B. and De Hoon, M.J.L.},
  Journal                  = {Bioinformatics},
  Year                     = {2009},
  Number                   = {11},
  Pages                    = {1422--1423},
  Volume                   = {25}
}

@Article{gatk2,
  Title                    = {A framework for variation discovery and genotyping using next-generation DNA sequencing data},
  Author                   = {DePristo, Mark A and Banks, Eric and Poplin, Ryan and Garimella, Kiran V and Maguire, Jared R and Hartl, Christopher and Philippakis, Anthony A and del Angel, Guillermo and Rivas, Manuel A and Hanna, Matt and McKenna, Aaron and Fennell, Tim J and Kernytsky, Andrew M and Sivachenko, Andrey Y and Cibulskis, Kristian and Gabriel, Stacey B and Altshuler, David and Daly, Mark J},
  Journal                  = {Nat. Genet.},
  Year                     = {2011},

  Month                    = may,
  Number                   = {5},
  Pages                    = {491--498},
  Volume                   = {43},

  Doi                      = {10.1038/ng.806},
  Url                      = {http://dx.doi.org/10.1038/ng.806}
}

@Article{clonalframeml,
  Title                    = {ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes},
  Author                   = {Didelot, Xavier and Wilson, Daniel J.},
  Journal                  = {PLoS Comput. Biol.},
  Year                     = {2015},

  Month                    = feb,
  Number                   = {2},
  Pages                    = {e1004041--},
  Volume                   = {11},

  Doi                      = {10.1371/journal.pcbi.1004041},
  Url                      = {http://dx.doi.org/10.1371%2Fjournal.pcbi.1004041}
}

@Article{phyml,
  Title                    = {New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0},
  Author                   = {Guindon, S. and Dufayard, J.F. and Lefort, V. and Anisimova, M. and Hordijk, W. and Gascuel O.},
  Journal                  = {Syst. Biol.},
  Year                     = {2010},
  Pages                    = {307--21},
  Volume                   = {59}
}

@Electronic{sickle,
  Title                    = {Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.29)},
  Author                   = {Joshi, N A and Fass, J N},
  HowPublished             = {github.com},
  Url                      = {https://github.com/najoshi/sickle},
  Year                     = {2011}
}

@Article{bwa,
  Title                    = {Fast and accurate short read alignment with Burrows–Wheeler transform},
  Author                   = {Li, Heng and Durbin, Richard},
  Journal                  = {Bioinformatics},
  Year                     = {2009},
  Number                   = {14},
  Pages                    = {1754--1760},
  Volume                   = {25},

  Doi                      = {10.1093/bioinformatics/btp324},
  Eprint                   = {http://bioinformatics.oxfordjournals.org/content/25/14/1754.full.pdf+html},
  Url                      = {http://bioinformatics.oxfordjournals.org/content/25/14/1754.abstract}
}

@Article{samtools,
  Title                    = {The Sequence Alignment/Map format and SAMtools},
  Author                   = {Li, H. and Handsaker, B. and Wysoker, A. and Fennell, T. and Ruan, J. and Homer, N. and Marth, G. and Abecasis, G. and Durbin, R.},
  Journal                  = {Bioinformatics},
  Year                     = {2009},

  Month                    = {Aug},
  Number                   = {16},
  Pages                    = {2078--2079},
  Volume                   = {25}
}

@Article{cutadapt,
  Title                    = {Cutadapt removes adapter sequences from high-throughput sequencing reads},
  Author                   = {Marcel Martin},
  Journal                  = {EMBnet.journal},
  Year                     = {2011},
  Number                   = {1},
  Pages                    = {1},
  Volume                   = {17}
}

@Article{gemsim,
  Title                    = {GemSIM: general, error-model based simulator of next-generation sequencing data},
  Author                   = {McElroy, K. E. and Luciani, F. and Thomas, T.},
  Journal                  = {BMC Genomics},
  Year                     = {2012},
  Pages                    = {74},
  Volume                   = {13}
}

@Article{gatk1,
  Title                    = {The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data},
  Author                   = {McKenna, Aaron and Hanna, Matthew and Banks, Eric and Sivachenko, Andrey and Cibulskis, Kristian and Kernytsky, Andrew and Garimella, Kiran and Altshuler, David and Gabriel, Stacey and Daly, Mark and DePristo, Mark A.},
  Journal                  = {Genome Res.},
  Year                     = {2010},
  Number                   = {9},
  Pages                    = {1297--1303},
  Volume                   = {20},

  Doi                      = {10.1101/gr.107524.110},
  Eprint                   = {http://genome.cshlp.org/content/20/9/1297.full.pdf+html},
  Url                      = {http://genome.cshlp.org/content/20/9/1297.abstract}
}

@Article{dendropy,
  Title                    = {DendroPy: a Python library for phylogenetic computing},
  Author                   = {Sukumaran, Jeet and Holder, Mark T.},
  Journal                  = {Bioinformatics},
  Year                     = {2010},

  Month                    = jun,
  Number                   = {12},
  Pages                    = {1569--1571},
  Volume                   = {26},

  Doi                      = {10.1093/bioinformatics/btq228},
  Url                      = {http://bioinformatics.oxfordjournals.org/content/26/12/1569.abstract}
}

@Article{discosnp,
  Title                    = {Reference-free detection of isolated SNPs},
  Author                   = {Uricaru, Raluca and Rizk, Guillaume and Lacroix, Vincent and Quillery, Elsa and Plantard, Olivier and Chikhi, Rayan and Lemaitre, Claire and Peterlongo, Pierre},
  Journal                  = {Nucleic Acids Res.},
  Year                     = {2015},
  Number                   = {2},
  Pages                    = {e11},
  Volume                   = {43},

  Doi                      = {10.1093/nar/gku1187},
  Eprint                   = {http://nar.oxfordjournals.org/content/43/2/e11.full.pdf+html},
  Url                      = {http://nar.oxfordjournals.org/content/43/2/e11.abstract}
}

@Article{gatk3,
  Title                    = {From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline},
  Author                   = {Van der Auwera, Geraldine A. and Carneiro, Mauricio O. and Hartl, Christopher and Poplin, Ryan and del Angel, Guillermo and Levy-Moonshine, Ami and Jordan, Tadeusz and Shakir, Khalid and Roazen, David and Thibault, Joel and Banks, Eric and Garimella, Kiran V. and Altshuler, David and Gabriel, Stacey and DePristo, Mark A.},
  Journal                  = {Curr. Protoc. Bioinform.},
  Year                     = {2013},
  Pages                    = {11.10.1--11.10.33},
  Volume                   = {43},

  Booktitle                = {Current Protocols in Bioinformatics},
  Chapter                  = {From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline},
  Doi                      = {10.1002/0471250953.bi1110s43},
  ISBN                     = {9780471250951},
  Series                   = {Current Protocols in Bioinformatics},
  Url                      = {http://dx.doi.org/10.1002/0471250953.bi1110s43}
}

@Article{baga,
  Title                    = {Refined analyses suggest that recombination is a minor source of genomic diversity in Pseudomonas aeruginosa chronic cystic fibrosis infections},
  Author                   = {Williams, David and Paterson, Steve and Brockhurst, Michael A and Winstanley, Craig},
  Journal                  = {Microbial Genomics},
  Year                     = {2016},

  Month                    = jan,

  Doi                      = {10.1099/mgen.0.000051},
  Url                      = {http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000051.v1}
}

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