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

Bioinformatics (Oxford, England) 2022 May 13

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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. 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. Accessible at https://hub.docker.com/r/lsbnb/metasquare_db and https://github.com/lsbnb/MetaSquare. Supplementary data are available at Bioinformatics online. © The Author(s) 2022. Published by Oxford University Press.

Citation

Chun-Chieh Liao, Po-Ying Fu, Chih-Wei Huang, Chia-Hsien Chuang, Yun Yen, Chung-Yen Lin, Shu-Hwa Chen. MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification. Bioinformatics (Oxford, England). 2022 May 13;38(10):2930-2931