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

ABSTRACT: 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.

SUBMITTER: Nasko DJ

PROVIDER: S-EPMC6206640 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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

Nasko Daniel J DJ Koren Sergey S Phillippy Adam M AM Treangen Todd J TJ

Genome biology 20181030 1

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 ...[more]

PMID: 30373669

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