ArticleStandards in genomic sciences2014
Quality scores for 32,000 genomes.
Article in Standards in genomic sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 43 citations in OpenAlex.
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- ProdMX: Rapid query and analysis of protein functional domain based on compressed sparse matrices.Computational and structural biotechnology journal · 2020Article
- Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.Nature communications · 2019Article
- FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science.Nature communications · 2019Article
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- Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale.Genome biology and evolution · 2018Article
- Pan4Draft: A Computational Tool to Improve the Accuracy of Pan-Genomic Analysis Using Draft Genomes.Scientific reports · 2018Article
- Article
- dBBQs: dataBase of Bacterial Quality scores.BMC bioinformatics · 2017Article
- Assessment of genome annotation using gene function similarity within the gene neighborhood.BMC bioinformatics · 2017Article
- Genomic characterization of Nontuberculous Mycobacteria.Scientific reports · 2017Article
- The hidden perils of read mapping as a quality assessment tool in genome sequencing.Scientific reports · 2017Article
- Analysis of Draft Genome Sequence ofBioMed research international · 2017Article
- The landscape of microbial phenotypic traits and associated genes.Nucleic acids research · 2016Article
- Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters.Microbiology (Reading, England) · 2016Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMore 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.
resultsScores 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.
conclusionsThe 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.