Quality scores for 32,000 genomes

Standards in Genomic Sciences
Miriam L LandDavid W Ussery

Abstract

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. 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 tool...Continue Reading

References

Nov 12, 2002·Journal of Bacteriology·Claire M FraserSteven L Salzberg
Apr 25, 2007·Nucleic Acids Research·Karin LagesenDavid W Ussery
Aug 14, 2008·PloS One·Helena F DeusJonas S Almeida
Nov 6, 2008·Nucleic Acids Research·Patricia P Chan, Todd M Lowe
Oct 10, 2009·Science·P S G ChainJ C Detter
Mar 10, 2010·BMC Bioinformatics·Doug HyattLoren J Hauser
May 20, 2011·Nucleic Acids Research·Robert D FinnSean R Eddy
Sep 8, 2011·Infection and Immunity·Joseph J GillespieBruno W Sobral
Jan 13, 2012·Journal of Clinical Microbiology·Mette V LarsenOle Lund
Nov 30, 2012·Nucleic Acids Research·Dennis A BensonEric W Sayers
Jul 5, 2013·Genome Biology·Richard J RobertsMichael C Schatz
Nov 30, 2013·Nucleic Acids Research·Robert D FinnMarco Punta

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Citations

Mar 28, 2017·Scientific Reports·Tarcisio FedrizziNicola Segata
Feb 28, 2015·Functional & Integrative Genomics·Miriam LandDavid W Ussery
Jan 4, 2018·BMC Bioinformatics·Visanu WanchaiDavid Ussery
Aug 21, 2019·Frontiers in Microbiology·Stephen L W OnGlen P Carter
Jul 17, 2016·Applied and Environmental Microbiology·Sagar M UtturkarDale A Pelletier
Jul 10, 2018·Genome Biology and Evolution·Gaelle BischSiv G E Andersson
Feb 18, 2016·Pathogens and Global Health·Stefano GaiarsaDavide Sassera
Jan 1, 2015·Bioinformatics and Biology Insights·Stefan E SeemannJan Gorodkin
Dec 5, 2016·Nucleic Acids Research·Maria BrbićFran Supek
Oct 27, 2015·Frontiers in Microbiology·Md Habibur RahamanMunirul Alam
Dec 19, 2020·Computational and Structural Biotechnology Journal·Visanu WanchaiDavid W Ussery
Jan 28, 2021·Communications Biology·Kaleb AbramDavid W Ussery

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Software Mentioned

GenBank Sequence Read Archive
KBase
Prodigal
HMMER3
Broad
SOLID
PATRIC
Broad Olive
Fasta
SE

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