MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification

Chun-Chieh Liao, Po-Ying Fu, Chih-Wei Huang, Chia-Hsien Chuang, Yun Yen, Chung-Yen Lin, Shu-Hwa Chen

Research output: Contribution to journalArticlepeer-review

Abstract

MOTIVATION: Taxonomic classification of 16S ribosomal RNA gene amplicon is an efficient and economic approach in microbiome analysis. 16S rRNA sequence databases like SILVA, RDP, EzBioCloud and HOMD used in downstream bioinformatic pipelines have limitations on either the sequence redundancy or the delay on new sequence recruitment. To improve the 16S rRNA gene-based taxonomic classification, we merged these widely used databases and a collection of novel sequences systemically into an integrated resource.

RESULTS: MetaSquare version 1.0 is an integrated 16S rRNA sequence database. It is composed of more than 6 million sequences and improves taxonomic classification resolution on both long-read and short-read methods.

AVAILABILITY AND IMPLEMENTATION: Accessible at https://hub.docker.com/r/lsbnb/metasquare_db and https://github.com/lsbnb/MetaSquare.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original languageEnglish
Pages (from-to)2930-2931
Number of pages2
JournalBioinformatics (Oxford, England)
Volume38
Issue number10
DOIs
Publication statusPublished - May 13 2022

Keywords

  • Genes, rRNA
  • Microbiota/genetics
  • Phylogeny
  • RNA, Ribosomal, 16S/genetics
  • Sequence Analysis, DNA/methods

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