Quality scores for 32,000 genomes
Miriam L. Land, Doug Hyatt, Se-Ran Jun, Guruprasad H. Kora, Loren J. Hauser, Oksana Lukjancenko, and David W. Ussery
2014 December 08, Standards in Genomic Sciences 2014, 9:20 doi:10.1186/1944-3277-9-20
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.
Land et al.: Quality scores for 32,000 genomes.
Standards in Genomic Sciences 2014 9:20.
Oak Ridge National Laboratory is managed by UT-Battelle for the Department of Energy