F1000Research (May 2024)
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 2; peer review: 1 approved, 2 approved with reservations]
- Olivia S. Smith,
- Ophélie Lebrasseur,
- Nihan D. Dagtas,
- Nikolay Oskolkov,
- Miriam J. Bravo-Lopez,
- Mohamed S. Sarhan,
- Megan Michel,
- Meriam van Os,
- Maria Lopopolo,
- Markella Moraitou,
- Kelly E. Blevins,
- Kevin G. Daly,
- Julien Fumey,
- Kadir T. Özdoğan,
- Jasmin Frangenberg,
- Javier G. Serrano,
- James A. Fellows Yates,
- Valentina Vanghi,
- Christina Warinner,
- Sally Wasef,
- Shreya L. Ramachandran,
- Piotr Rozwalak,
- Raphael Eisenhofer,
- Maxime Borry,
- Irina M. Velsko,
- Iseult Jackson,
- I-Ting Huang,
- Ian Light,
- Gabriel Yaxal Ponce-Soto,
- Gunnar Neumann,
- Bjørn Peare Bartholdy,
- Diāna Spurīte,
- Arthur Kocher,
- Åshild J. Vågene,
- Andrea Quagliariello,
- Anna E. White,
- Alexander Hübner,
- Anan Ibrahim,
- Adrian Forsythe,
- Aida Andrades Valtueña
Affiliations
- Olivia S. Smith
- Department of Integrative Biology, The University of Texas at Austin, Speedway 2415, Austin, Texas, 78712, USA
- Ophélie Lebrasseur
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, 3 de Febrero 1370 (1426), Ciudad Autónoma de Buenos Aires, C1426BJN CABA, Argentina
- Nihan D. Dagtas
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv-Yafo, 69978, Israel
- Nikolay Oskolkov
- ORCiD
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Tomtebodavägen 23, Stockholm, 17165, Sweden
- Miriam J. Bravo-Lopez
- International Laboratory for Human Genome Research (LIIGH), Universidad Nacional Autonoma de Mexico, La Mesa 3001, Juriquilla, Queretaro, 76230, Mexico
- Mohamed S. Sarhan
- ORCiD
- Institute for Mummy Studies, Eurac Research, Drususallee 1, Bolzano/Bozen, Autonome Provinz Bozen, 39100, Italy
- Megan Michel
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Meriam van Os
- ORCiD
- Department of Anatomy, University of Otago, 270 Great King St, Dunedin, Otago, 9016, New Zealand
- Maria Lopopolo
- ORCiD
- Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France
- Markella Moraitou
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, Scotland, EH9 3FL, UK
- Kelly E. Blevins
- Center for Bioarchaeological Research, Arizona State University, Candy Mall, Tempe, Arizona, 85281, USA
- Kevin G. Daly
- Smurfit Institute of Genetics, The University of Dublin Trinity College, Dublin, Leinster, D02 VF25, Ireland
- Julien Fumey
- ORCiD
- Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France
- Kadir T. Özdoğan
- Animal Ecology, Wageningen Environmental Research, P.O box 47, Wageningen, Gelderland, 6700 AA, The Netherlands
- Jasmin Frangenberg
- ORCiD
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
- Javier G. Serrano
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, 38200, Spain
- James A. Fellows Yates
- ORCiD
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Valentina Vanghi
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv-Yafo, 69978, Israel
- Christina Warinner
- ORCiD
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Sally Wasef
- ORCiD
- Defence Genomics, Centre for Genomics and Personalised Health, Queensland University of Technology, Musk Ave 60, Kelvin Grove, Queensland, 4059, Australia
- Shreya L. Ramachandran
- ORCiD
- Department of Human Genetics, The University of Chicago, E. 58th St. 920, Chicago, Illinois, 60637, USA
- Piotr Rozwalak
- Department of Computational Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznanskiego 6, Poznań, Wielkopolska, 61-614, Poland
- Raphael Eisenhofer
- Center for Evolutionary Hologenomics, Globe Institute, Københavns Universitet, ester Voldgade 44747, Copenhagen, Copenhagen K, 1350, Denmark
- Maxime Borry
- ORCiD
- 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
- Irina M. Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Iseult Jackson
- ORCiD
- SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway, H91 TK33, Ireland
- I-Ting Huang
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, Massachusetts, 02138, USA
- Ian Light
- Max Planck Institute for Infection Biology, Virchowweg 12, Berlin, Berlin, 10117, Germany
- Gabriel Yaxal Ponce-Soto
- Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015, France
- Gunnar Neumann
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Bjørn Peare Bartholdy
- ORCiD
- Department of Archaeological Sciences, Universiteit Leiden, Einsteinweg 2, Leiden, 2333 CC, The Netherlands
- Diāna Spurīte
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Arthur Kocher
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Åshild J. Vågene
- Section for Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, Københavns Universitet, Oester Voldgade 44747, Copenhagen K, 1350, Denmark
- Andrea Quagliariello
- Department of Comparative Biomedicine and Food Science, Universita degli Studi di Padova, Viale dell'Università 16, Legnaro, Padova, 350250, Italy
- Anna E. White
- ORCiD
- Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, Københavns Universitet, Øster Farimagsgade 5, Copenhagen K, 1353, Denmark
- Alexander Hübner
- 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
- Anan Ibrahim
- ORCiD
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745, Germany
- Adrian Forsythe
- Department of Animal Zoology, Uppsala Universitet, Norbyvägen 18D, Uppsala, 752 36, Sweden
- Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103, Germany
- Journal volume & issue
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Vol. 12
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.
