RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k -mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatl...

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Vydáno v:Genome Biology Ročník 19; číslo 1; s. 165
Hlavní autoři: Nasko, Daniel J., Koren, Sergey, Phillippy, Adam M., Treangen, Todd J.
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 30.10.2018
Springer Nature B.V
BMC
Témata:
ancestry
Animal Genetics and Genomics
Bayesian analysis
Bioinformatics
Biomedical and Life Sciences
Classification
Comparative analysis
Datasets
Evolutionary Biology
Genera
genome
Genomes
Human Genetics
Identification
Influence
k-mer
Life Sciences
Metagenomics
Methods
Microbial Genetics and Genomics
Microbiome
New genera
New species
Open Letter
Performance evaluation
Plant Genetics and Genomics
Reference database
species identification
Taxonomic classification
Taxonomy
Metagenomics
Taxonomic classification
Reference database
mer
LCA
Comparative analysis
Microbiome
k-mer
ISSN:1474-760X, 1474-7596, 1474-760X
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Shrnutí:In order to determine the role of the database in taxonomic sequence classification, we examine the influence of the database over time on k -mer-based lowest common ancestor taxonomic classification. We present three major findings: the number of new species added to the NCBI RefSeq database greatly outpaces the number of new genera; as a result, more reads are classified with newer database versions, but fewer are classified at the species level; and Bayesian-based re-estimation mitigates this effect but struggles with novel genomes. These results suggest a need for new classification approaches specially adapted for large databases.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-018-1554-6