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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; Spurite, Diana; Ponce-Soto, Gabriel Yaxal; Neumann, Gunnar; Huang, I-Ting; Light, Ian; Velsko, Irina M; Jackson, Iseult; Frangenberg, Jasmin; Serrano, Javier G; Fumey, Julien; Özdogan, 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.
Afiliação
  • Borry M; Cluster of Excellence "Balance of the Microverse", Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany.
  • Forsythe A; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • Andrades Valtueña A; Department of Animal Zoology, Uppsala Universitet, Norbyvägen 18D, Uppsala, 752 36, Sweden.
  • Hübner A; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • Ibrahim A; Cluster of Excellence "Balance of the Microverse", Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany.
  • Quagliariello A; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • White AE; Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany.
  • Kocher A; Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany.
  • Vågene ÅJ; Department of Comparative Biomedicine and Food Science, Universita degli Studi di Padova, Viale dell'Università 16, Legnaro, Padova, 350250, Italy.
  • Bartholdy BP; Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, Københavns Universitet, Øster Farimagsgade 5, Copenhagen K, 1353, Denmark.
  • Spurite D; BioArCh, Department of Archaeology, University of York, York, England, YO10 5DD, UK.
  • Ponce-Soto GY; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • Neumann G; Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for Geoanthropology, Kahlaische Str. 10, Jena, Thuringia, 07745, Germany.
  • Huang IT; Section for Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, Københavns Universitet, Oester Voldgade 44747, Copenhagen K, 1350, Denmark.
  • Light I; Department of Archaeological Sciences, Universiteit Leiden, Einsteinweg 2, Leiden, 2333 CC, The Netherlands.
  • Velsko IM; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • Jackson I; Institute of Ecology and Evolution, Friedrich-Schiller-Universität Jena, Jena, Thuringia, 07743, Germany.
  • Frangenberg J; Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France.
  • Serrano JG; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • Fumey J; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • Özdogan KT; Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, Massachusetts, 02138, USA.
  • Blevins KE; Max Planck Institute for Infection Biology, Virchowweg 12, Berlin, Berlin, 10117, Germany.
  • Daly KG; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • Lopopolo M; SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway, H91 TK33, Ireland.
  • Moraitou M; Smurfit Institute of Genetics, The University of Dublin Trinity College, Dublin, Leinster, D02 VF25, Ireland.
  • Michel M; Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany.
  • van Os M; Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, 38200, Spain.
  • Bravo-Lopez MJ; Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France.
  • Sarhan MS; Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France.
  • Dagtas ND; Animal Ecology, Wageningen Environmental Research, P.O box 47, Wageningen, Gelderland, 6700 AA, The Netherlands.
  • Oskolkov N; Department of History and Art History, Universiteit Utrecht, Drift 6, Utrecht, Utrecht, 3512 BS, The Netherlands.
  • Smith OS; Center for Bioarchaeological Research, Arizona State University, Candy Mall, Tempe, Arizona, 85281, USA.
  • Lebrasseur O; Department of Archaeology, Durham University, South Road, Durham, County Durham, England, DH1 3LE, UK.
  • Rozwalak P; Smurfit Institute of Genetics, The University of Dublin Trinity College, Dublin, Leinster, D02 VF25, Ireland.
  • Eisenhofer R; Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France.
  • Wasef S; Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, Scotland, EH9 3FL, UK.
  • Ramachandran SL; Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • Vanghi V; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany.
  • Warinner C; Department of Human Evolutionary Biology, Harvard University, Divinity Avenue 11, Cambridge, Massachusetts, 02138, USA.
  • Fellows Yates JA; Department of Anatomy, University of Otago, 270 Great King St, Dunedin, Otago, 9016, New Zealand.
F1000Res ; 12: 926, 2023.
Article em En | MEDLINE | ID: mdl-39262445
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.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Metagenômica / Metadados Idioma: En Ano de publicação: 2023 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Metagenômica / Metadados Idioma: En Ano de publicação: 2023 Tipo de documento: Article