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

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dc.contributor.authorBorry, M.
dc.contributor.authorForsythe, A.
dc.contributor.authorAndrades Valtueña, A.
dc.contributor.authorHübner, A.
dc.contributor.authorIbrahim, A.
dc.contributor.authorQuagliariello, A.
dc.contributor.authorWhite, A.E.
dc.contributor.authorKocher, A.
dc.contributor.authorVågene‬, Å.J.
dc.contributor.authorBartholdy, B.P.
dc.contributor.authorSpurīte, D.
dc.contributor.authorPonce-Soto, G.Y.
dc.contributor.authorNeumann, G.
dc.contributor.authorHuang, I.T.
dc.contributor.authorLight, I.
dc.contributor.authorVelsko, I.M.
dc.contributor.authorJackson, I.
dc.contributor.authorFrangenberg, J.
dc.contributor.authorSerrano, J.G.
dc.contributor.authorFumey, J.
dc.contributor.authoret al.
dc.date.issued2024
dc.description.abstractBackground: 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 librarylevel 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.
dc.identifier.citationF1000Research, 2024; 12:926-1-926-35
dc.identifier.doi10.12688/f1000research.134798.2
dc.identifier.issn2046-1402
dc.identifier.issn2046-1402
dc.identifier.urihttps://hdl.handle.net/2440/146610
dc.language.isoen
dc.publisherF1000 Research Ltd
dc.rights© 2024 Borry M et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.source.urihttps://doi.org/10.12688/f1000research.134798.2
dc.subjectmetagenomics; environmental; palaeogenomics; aDNA; microbiome; metadata; microbial; FAIR data
dc.subject.meshHumans
dc.subject.meshComputational Biology
dc.subject.meshSoftware
dc.subject.meshMetagenome
dc.subject.meshMetagenomics
dc.subject.meshHigh-Throughput Nucleotide Sequencing
dc.subject.meshMetadata
dc.subject.meshDNA, Ancient
dc.titleFacilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. [version 2; peer reviewed: 1 approved, 3 approved with reservations]
dc.title.alternativeFacilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.
dc.typeJournal article
pubs.publication-statusPublished

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