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Understanding trivial challenges of microbial genomics: An assembly example

Delphine Lariviere, Han Mei, Mallory Freeberg, View ORCID ProfileJames Taylor, View ORCID ProfileAnton Nekrutenko
doi: https://doi.org/10.1101/347625
Delphine Lariviere
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University
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Han Mei
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University
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Mallory Freeberg
2European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, UK
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James Taylor
3Department of Biology and Computer Science, Johns Hopkins University
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Anton Nekrutenko
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University
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  • ORCID record for Anton Nekrutenko
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Abstract

The perceived “simplicity” of bacterial genomics (these genomes are small and easy to assemble) feeds the decentralized state of the field where computational analysis standards have been slow to evolve. This situation has a historical explanation. In cases of human, mouse, fly, worm and other model organisms there have been large sustained multinational genome sequencing efforts and analysis consortia such as the 1,000 genomes, ENCODE, modENCODE, GTEx and others. These resulted in development and proliferation of common tools, workflows, and data standards. This is not the case in microbiology. After the development of highly parallel sequencing methodologies in mid-2000s bacterial genomes no longer required initiatives of such scale. The flipside of this is the extreme heterogeneity of approaches to many well established microbial genomic analysis problems such as genome assembly. While competition amongst different methods is good, we argue that the quality of data analyses will improve if cutting edge tools are more accessible and microbiologists become more computationally savvy. Here we use genome assembly as an example to highlight current challenges and to provide a possible solution.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 14, 2018.
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Understanding trivial challenges of microbial genomics: An assembly example
Delphine Lariviere, Han Mei, Mallory Freeberg, James Taylor, Anton Nekrutenko
bioRxiv 347625; doi: https://doi.org/10.1101/347625
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Understanding trivial challenges of microbial genomics: An assembly example
Delphine Lariviere, Han Mei, Mallory Freeberg, James Taylor, Anton Nekrutenko
bioRxiv 347625; doi: https://doi.org/10.1101/347625

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