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

doi:10.1093/bioinformatics/btac184

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

臺北醫學大學癌症轉譯研究中心

研究成果: 雜誌貢獻 › 文章 › 同行評審

6 引文斯高帕斯（Scopus）

摘要

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.

原文	英語
頁（從 - 到）	2930-2931
頁數	2
期刊	Bioinformatics (Oxford, England)
卷	38
發行號	10
DOIs	https://doi.org/10.1093/bioinformatics/btac184
出版狀態	已發佈 - 5月 13 2022

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10.1093/bioinformatics/btac184

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title = "MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification",

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.",

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

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year = "2022",

month = may,

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doi = "10.1093/bioinformatics/btac184",

language = "English",

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T2 - an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification

AU - Liao, Chun-Chieh

AU - Fu, Po-Ying

AU - Huang, Chih-Wei

AU - Chuang, Chia-Hsien

AU - Yen, Yun

AU - Lin, Chung-Yen

AU - Chen, Shu-Hwa

N1 - © The Author(s) 2022. Published by Oxford University Press.

PY - 2022/5/13

Y1 - 2022/5/13

N2 - 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.

AB - 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.

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KW - Microbiota/genetics

KW - Phylogeny

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KW - Sequence Analysis, DNA/methods

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DO - 10.1093/bioinformatics/btac184

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JO - Bioinformatics (Oxford, England)

JF - Bioinformatics (Oxford, England)

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ER -

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

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