Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT

Borry, Maxime; Forsythe, Adrian; Andrades Valtueña, Aida; Hübner, Alexander; Ibrahim, Anan; Quagliariello, Andrea; White, Anna E.; Kocher, Arthur; Vågene‬, Åshild J.; Bartholdy, Bjørn Peare; Spurīte, Diāna; Ponce-Soto, Gabriel Yaxal; Neumann, Gunnar; Huang, I-Ting; Light, Ian; Velsko, Irina M.; Jackson, Iseult; Frangenberg, Jasmin; Serrano, Javier G.; Fumey, Julien; Özdoğan, Kadir T.; Blevins, Kelly E.; Daly, Kevin G.; Lopopolo, Maria; Moraitou, Markella; Michel, Megan; van Os, Meriam; Bravo-Lopez, Miriam J.; Sarhan, Mohamed S.; Dagtas, Nihan D.; Oskolkov, Nikolay; Smith, Olivia S.; Lebrasseur, Ophélie; Rozwalak, Piotr; Eisenhofer, Raphael; Wasef, Sally; Ramachandran, Shreya L.; Vanghi, Valentina; Warinner, Christina; Fellows Yates, James A.

Abstract

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.org) 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 rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.

Results
AncientMetagenomeDir was extended to include standardised metadata of over 6000 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 reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.

Citation

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., …Fellows Yates, J. A. (2024). Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. F1000Research, 12, Article 926. https://doi.org/10.12688/f1000research.134798.2

• Journal Article Type: Article
• Acceptance Date: Apr 28, 2024
• Online Publication Date: May 28, 2024
• Publication Date: 2024-11
• Deposit Date: Nov 14, 2024
• Publicly Available Date: Nov 14, 2024
• Journal: F1000Research
• Electronic ISSN: 2046-1402
• Publisher: Taylor and Francis
• Peer Reviewed: Peer Reviewed
• Volume: 12
• Article Number: 926
• DOI: https://doi.org/10.12688/f1000research.134798.2
• Public URL: https://durham-repository.worktribe.com/output/3094984