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  Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 2; peer review: 1 approved, 3 approved with reservations]

Borry, M., Forsythe, A., Andrades Valtueña, A., Hübner, A., Ibrahim, A., Quagliariello, A., White, A. E., Kocher, A., Vågene, Å. J., Bartholdy, B. P., Spurīte, D., Ponce-Soto, G. Y., Neumann, G., Huang, I.-T., Light, I., Velsko, I. M., Jackson, I., Frangenberg, J., Serrano, J. G., Fumey, J., Özdoğan, K. T., Blevins, K. E., Daly, K. G., Lopopolo, M., Moraitou, M., Michel, M., van Os, M., Bravo-Lopez, M. J., Sarhan, M. S., Dagtas, N. D., Oskolkov, N., Smith, O. S., Lebrasseur, O., Rozwalak, P., Eisenhofer, R., Wasef, S., Ramachandran, S. L., Vanghi, V., Warinner, C. G., & Fellows Yates, J. A. (2023). Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 2; peer review: 1 approved, 3 approved with reservations]. F1000Research, 12:. doi:10.12688/f1000research.134798.2.

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基本情報

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アイテムのパーマリンク: https://hdl.handle.net/21.11116/0000-000F-1344-F 版のパーマリンク: https://hdl.handle.net/21.11116/0000-0010-35D0-7
資料種別: 学術論文

ファイル

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:
Borry_Faciliating_F1000Research_2023.pdf (出版社版), 4MB
ファイルのパーマリンク:
https://hdl.handle.net/21.11116/0000-000F-1371-C
ファイル名:
Borry_Faciliating_F1000Research_2023.pdf
説明:
-
OA-Status:
Gold
閲覧制限:
公開
MIMEタイプ / チェックサム:
application/pdf / [MD5]
技術的なメタデータ:
著作権日付:
2023
著作権情報:
-

関連URL

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URL:
https://pypi.org/project/AMDirT/ (付録資料)
説明:
Software (Code)
OA-Status:
Green
説明:
Source Data
OA-Status:
Green
説明:
Underlying Data
OA-Status:
Green

作成者

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 作成者:
Borry, Maxime1, 著者                 
Forsythe, Adrian, 著者
Andrades Valtueña, Aida1, 著者                 
Hübner, Alexander1, 著者                 
Ibrahim, Anan, 著者
Quagliariello, Andrea, 著者
White, Anna E., 著者
Kocher, Arthur1, 著者                 
Vågene, Åshild J., 著者
Bartholdy, Bjørn Peare, 著者
Spurīte, Diāna1, 著者           
Ponce-Soto, Gabriel Yaxal, 著者
Neumann, Gunnar1, 2, 著者                 
Huang, I-Ting, 著者
Light, Ian, 著者
Velsko, Irina M.1, 著者                 
Jackson, Iseult, 著者
Frangenberg, Jasmin, 著者
Serrano, Javier G., 著者
Fumey, Julien, 著者
Özdoğan, Kadir T., 著者Blevins, Kelly E., 著者Daly, Kevin G., 著者Lopopolo, Maria, 著者Moraitou, Markella, 著者Michel, Megan1, 著者                 van Os, Meriam, 著者Bravo-Lopez, Miriam J., 著者Sarhan, Mohamed S., 著者Dagtas, Nihan D., 著者Oskolkov, Nikolay, 著者Smith, Olivia S., 著者Lebrasseur, Ophélie, 著者Rozwalak, Piotr, 著者Eisenhofer, Raphael, 著者Wasef, Sally, 著者Ramachandran, Shreya L., 著者Vanghi, Valentina, 著者Warinner, Christina G.1, 著者                 Fellows Yates, James A.1, 著者                  全て表示
所属:
1Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society, ou_3222712              
2MHAAM, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Max Planck Society, ou_3390638              

内容説明

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キーワード: metagenomics,environmental,palaeogenomics,aDNA,microbiome,metadata,microbial,FAIR data
 要旨: Background: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.github.io) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.

Methods: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate automated metadata curation and data validation, as well as rapid data filtering and downloading.

Results: AncientMetagenomeDir was extended to include standardised metadata of over 5000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.

Conclusions: Together, both standardised metadata and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.

資料詳細

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言語: eng - English
 日付: 2023-08-02
 出版の状態: オンラインで出版済み
 ページ: 15
 出版情報: -
 目次: Introduction
Methods
- Implementation
- Operation
Use cases
Discussion
- Results of library level metadata aggregation
- Common issues in ancient metagenomic library metadata
- Note on AMDirT generated pipeline scripts
- Future development
Data availability
- Source data
- Software availability
 査読: 査読あり
 識別子(DOI, ISBNなど): DOI: 10.12688/f1000research.134798.2
 学位: -

関連イベント

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訴訟

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Project information

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Project name : DAIRYCULTURES
Grant ID : 804884
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)
Project name : PALEoRIDER
Grant ID : 771234
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)

出版物 1

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出版物名: F1000Research
種別: Web Page
 著者・編者:
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出版社, 出版地: -
ページ: - 巻号: 12 通巻号: 926 開始・終了ページ: - 識別子(ISBN, ISSN, DOIなど): URN: https://f1000research.com/