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dBBQs : dataBase of Bacterial Quality scores

Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew, David Ussery
doi: https://doi.org/10.1101/187641
Visanu Wanchai
1Arkansas Center for Genomic Epidemiology & Medicine and The Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
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Preecha Patumcharoenpol
1Arkansas Center for Genomic Epidemiology & Medicine and The Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
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Intawat Nookaew
1Arkansas Center for Genomic Epidemiology & Medicine and The Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
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David Ussery
1Arkansas Center for Genomic Epidemiology & Medicine and The Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
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Abstract

Background It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever growing large collections of genome sequences. However, it is less known that the majority of available sequenced genome sequences in public databases are not complete, drafts of varying qualities. We have calculated quality scores for around 100,000 bacterial genomes from all major genome repositories and put them in a fast and easy-to-use database.

Results Prokaryotic genomic data from all sources were collected and combined to make a non-redundant set of bacterial genomes. The genome quality score for each was calculated by four different measurements: assembly quality, number of rRNA and tRNA genes, and the occurrence of conserved functional domains. The dataBase of Bacterial Quality scores (dBBQs) was designed to store and retrieve quality scores. It offers fast searching and download features which the result can be used for further analysis. In addition, the search results are shown in interactive JavaScript chart framework using DC.js. The analysis of quality scores across major public genome databases find that around 68% of the genomes are of acceptable quality for many uses.

Conclusions dBBQs (available at http://arc-gem.uams.edu/dbbqs) provides genome quality scores for all available prokaryotic genome sequences with a user-friendly Web-interface. These scores can be used as cut-offs to get a high-quality set of genomes for testing bioinformatics tools or improving the analysis. Moreover, all data of the four measurements that were combined to make the quality score for each genome, which can potentially be used for further analysis. dBBQs will be updated regularly and is freely use for non-commercial purpose.

Footnotes

  • Email addresses: VW: vwanchai{at}uams.edu, PP: ppatumcharoenpol{at}uams.edu, IN: inookaew{at}uams.edu, DU: dwussery{at}uams.edu

  • List of abbreviations

    dBBQs
    dataBase of Bacterial Quality scores
    NCBI
    National Center for Biotechnology information
    Kbase
    The U.S. Department of Energy Systems Biology Knowledgebase
    PATRIC
    Pathosystems Resource Integration Center
    SRA
    Sequence Read Archive
    API
    Application program interface
    CSV
    Comma-separated Value.
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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    dBBQs : dataBase of Bacterial Quality scores
    Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew, David Ussery
    bioRxiv 187641; doi: https://doi.org/10.1101/187641
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    dBBQs : dataBase of Bacterial Quality scores
    Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew, David Ussery
    bioRxiv 187641; doi: https://doi.org/10.1101/187641

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