Quality scores for 32,000 genomes

Land, Miriam L.; Hyatt, Doug; Jun, Se-Ran; Kora, Guruprasad H.; Hauser, Loren J.; Lukjancenko, Oksana; Ussery, David W.

doi:10.1186/1944-3277-9-20

Title: Quality scores for 32,000 genomes

Journal Article · Mon Dec 08 00:00:00 EST 2014 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/1944-3277-9-20· OSTI ID:1185423

Land, Miriam L. ^[1]; Hyatt, Doug ^[2]; Jun, Se-Ran ^[1]; Kora, Guruprasad H. ^[3]; Hauser, Loren J. ^[4]; Lukjancenko, Oksana ^[5]; Ussery, David W. ^[6]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division. Comparative Genomics Group
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
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division
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
Technical Univ. of Denmark, Lyngby (Denmark). Center for Genomic Epidemiology
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

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 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. 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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Laboratory Directed Research and Development (LDRD)

Grant/Contract Number:: AC05-00OR22725; PS02-06ER64304

OSTI ID:: 1185423

Journal Information:: Standards in Genomic Sciences, Vol. 9; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 30 works

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