title: Quality scores for 32,000 genomes.
abstract: BACKGROUND
  More than 80% of the microbial genomes in GenBank are of 'draft' quality (12,553 draft vs. 2,679 finished, as of October, 2013). We have examined all the microbial DNA sequences available for complete, draft, and Sequence Read Archive genomes in GenBank as well as three other major public databases, and assigned quality scores for more than 30,000 prokaryotic genome sequences.
  
  
  RESULTS
  Scores were assigned using four categories: the completeness of the assembly, the presence of full-length rRNA genes, tRNA composition and the presence of a set of 102 conserved genes in prokaryotes. Most (~88%) of the genomes had quality scores of 0.8 or better and can be safely used for standard comparative genomics analysis. We compared genomes across factors that may influence the score. We found that although sequencing depth coverage of over 100x did not ensure a better score, sequencing read length was a better indicator of sequencing quality. With few exceptions, most of the 30,000 genomes have nearly all the 102 essential genes.
  
  
  CONCLUSIONS
  The score can be used to set thresholds for screening data when analyzing "all published genomes" and reference data is either not available or not applicable. The scores highlighted organisms for which commonly used tools do not perform well. This information can be used to improve tools and to serve a broad group of users as more diverse organisms are sequenced. Unexpectedly, the comparison of predicted tRNAs across 15,000 high quality genomes showed that anticodons beginning with an 'A' (codons ending with a 'U') are almost non-existent, with the exception of one arginine codon (CGU); this has been noted previously in the literature for a few genomes, but not with the depth found here.
authors.affiliation: Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS 6420, Oak Ridge, TN 37831-6420, USA.
authors.forename: Miriam L
authors.initials: ML
authors.lastname: Land
authors.affiliation: Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS 6420, Oak Ridge, TN 37831-6420, USA ; Joint Institute for Biological Sciences, University of Tennessee, Knoxville, TN 37996, USA.
authors.forename: Doug
authors.initials: D
authors.lastname: Hyatt
authors.affiliation: Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS 6420, Oak Ridge, TN 37831-6420, USA.
authors.forename: Se-Ran
authors.initials: SR
authors.lastname: Jun
authors.affiliation: Computer Science and Mathematics Division, Computer Science Research Group, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Guruprasad H
authors.initials: GH
authors.lastname: Kora
authors.affiliation: Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS 6420, Oak Ridge, TN 37831-6420, USA ; Joint Institute for Biological Sciences, University of Tennessee, Knoxville, TN 37996, USA ; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA.
authors.forename: Loren J
authors.initials: LJ
authors.lastname: Hauser
authors.affiliation: Center for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby 2800, Denmark.
authors.forename: Oksana
authors.initials: O
authors.lastname: Lukjancenko
authors.affiliation: Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS 6420, Oak Ridge, TN 37831-6420, USA ; Joint Institute for Biological Sciences, University of Tennessee, Knoxville, TN 37996, USA ; Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kgs. Lyngby 2800, Denmark.
authors.forename: David W
authors.initials: DW
authors.lastname: Ussery
keywords: DNA; Database; Evaluation; Quality; Sequencing; Status