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Title: Quality scores for 32,000 genomes

More than 80% of the microbial genomes in GenBank are of ‘draft’ quality (12,553 draft vs. 2,679 finished, as of October, 2013). In this study, 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. 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. 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 commonlymore » 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. Finally and 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.« less
Authors:
 [1] ;  [2] ;  [1] ;  [3] ;  [4] ;  [5] ;  [6]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division. Comparative Genomics Group
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division. Comparative Genomics Group; Univ. of Tennessee, Knoxville, TN (United States). Joint Inst. for Biological Sciences
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division
  4. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division. Comparative Genomics Group; Univ. of Tennessee, Knoxville, TN (United States). Joint Inst. for Biological Sciences; Univ. of Tennessee, Knoxville, TN (United States). Dept. of Microbiology
  5. Technical Univ. of Denmark, Lyngby (Denmark). Center for Genomic Epidemiology
  6. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division. Comparative Genomics Group; Univ. of Tennessee, Knoxville, TN (United States). Joint Inst. for Biological Sciences; Technical Univ. of Denmark, Lyngby (Denmark). Dept. of Systems Biology. Center for Biological Sequence Analysis
Publication Date:
OSTI Identifier:
1185423
Grant/Contract Number:
AC05-00OR22725; PS02-06ER64304
Type:
Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Laboratory Directed Research and Development (LDRD)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES DNA; sequencing; database; quality; evaluation; status