Peer Review Report For: Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT [version 2; peer review: 1 approved, 3 approved with reservations]
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.
Authors 40
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Maxime Borry corresponding
Max Planck Institute for Evolutionary Anthropology · Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI)
Affiliation as printed
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
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
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Affiliation as printed
Department of Animal Zoology, Uppsala Universitet, Norbyvägen 18D, Uppsala, 752 36
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Max Planck Institute for Evolutionary Anthropology
Affiliation as printed
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
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Max Planck Institute for Evolutionary Anthropology · Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI)
Affiliation as printed
Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745
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
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
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Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI)
Affiliation as printed
Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745
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Affiliation as printed
Department of Comparative Biomedicine and Food Science, Universita degli Studi di Padova, Viale dell'Università 16, Legnaro, Padova, 350250
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University of Copenhagen · University of York
Affiliation as printed
BioArCh, Department of Archaeology, University of York, York, England, YO10 5DD
Section for Molecular Ecology and Evolution, Globe Institute, Faculty of Health and Medical Sciences, Københavns Universitet, Øster Farimagsgade 5, Copenhagen K, 1353
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Max Planck Institute for Evolutionary Anthropology · Max Planck Institute of Geoanthropology
Affiliation as printed
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for Geoanthropology, Kahlaische Str. 10, Jena, Thuringia, 07745
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Affiliation as printed
Section for Hologenomics, Globe Institute, Faculty of Health and Medical Sciences, Københavns Universitet, Oester Voldgade 44747, Copenhagen K, 1350
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Affiliation as printed
Department of Archaeological Sciences, Universiteit Leiden, Einsteinweg 2, Leiden, 2333 CC
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Max Planck Institute for Evolutionary Anthropology · Friedrich Schiller University Jena
Affiliation as printed
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
Institute of Ecology and Evolution, Friedrich-Schiller-Universität Jena, Jena, Thuringia, 07743
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Centre National de la Recherche Scientifique · Institut Pasteur · Université Paris Cité · Génomique évolutive, modélisation et santé
Affiliation as printed
Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015
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Max Planck - Harvard Research Center for the Archaeoscience of the Ancient Mediterranean · Max Planck Institute for Evolutionary Anthropology
Affiliation as printed
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
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
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Affiliation as printed
Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, Massachusetts, 02138
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Max Planck Institute for Infection Biology
Affiliation as printed
Max Planck Institute for Infection Biology, Virchowweg 12, Berlin, Berlin, 10117
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Max Planck Institute for Evolutionary Anthropology
Affiliation as printed
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
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Ollscoil na Gaillimhe – University of Galway · Trinity College Dublin
Affiliation as printed
SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway, H91 TK33
Smurfit Institute of Genetics, The University of Dublin Trinity College, Dublin, Leinster, D02 VF25
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Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI)
Affiliation as printed
Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745
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Affiliation as printed
Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, 38200
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Centre National de la Recherche Scientifique · Institut Pasteur · Université Paris Cité · Génomique évolutive, modélisation et santé
Affiliation as printed
Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015
Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015
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Utrecht University · Wageningen University & Research
Affiliation as printed
Animal Ecology, Wageningen Environmental Research, P.O box 47, Wageningen, Gelderland, 6700 AA
Department of History and Art History, Universiteit Utrecht, Drift 6, Utrecht, Utrecht, 3512 BS
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Durham University · Arizona State University
Affiliation as printed
Center for Bioarchaeological Research, Arizona State University, Candy Mall, Tempe, Arizona, 85281
Department of Archaeology, Durham University, South Road, Durham, County Durham, England, DH1 3LE
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Affiliation as printed
Smurfit Institute of Genetics, The University of Dublin Trinity College, Dublin, Leinster, D02 VF25
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Centre National de la Recherche Scientifique · Institut Pasteur · Université Paris Cité · Génomique évolutive, modélisation et santé
Affiliation as printed
Microbial Paleogenomics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Rue du Docteur Roux 25-28, Paris, Île-de-France, F-75015
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Affiliation as printed
Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, Scotland, EH9 3FL
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Harvard University · Max Planck - Harvard Research Center for the Archaeoscience of the Ancient Mediterranean · Max Planck Institute for Evolutionary Anthropology
Affiliation as printed
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
Department of Human Evolutionary Biology, Harvard University, Divinity Avenue 11, Cambridge, Massachusetts, 02138
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
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Affiliation as printed
Department of Anatomy, University of Otago, 270 Great King St, Dunedin, Otago, 9016
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Universidad Nacional Autónoma de México
Affiliation as printed
Center for Genomic Sciences (CCG), Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, 62210
International Laboratory for Human Genome Research (LIIGH), Universidad Nacional Autonoma de Mexico, La Mesa 3001, Juriquilla, Queretaro, 76230
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Eurac Research · University of Trento
Affiliation as printed
Centre for Integrative Biology (CIBIO), Universita degli Studi di Trento, Via Sommarive 9, Povo, Trentino, 38123
Institute for Mummy Studies, Eurac Research, Drususallee 1, Bolzano/Bozen, Autonome Provinz Bozen, 39100
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Affiliation as printed
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
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Lund University · Science for Life Laboratory · National Bioinformatics Infrastructure Sweden
Affiliation as printed
Department of Biology, Lunds Universitet, Sölvegatan 35, Lund, 223 62
National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Tomtebodavägen 23, Stockholm, 17165
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The University of Texas at Austin
Affiliation as printed
Department of Integrative Biology, The University of Texas at Austin, Speedway 2415, Austin, Texas, 78712
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Centre National de la Recherche Scientifique · Université Toulouse III - Paul Sabatier · Centre d'Anthropobiologie et de Génomique de Toulouse
Affiliation as printed
Center for Anthropobiology and Genomics of Toulouse, CNRS/Universite Toulouse III Paul Sabatier, Allées Jules Guesde 37, Toulouse, Occitanie, 31000
Instituto Nacional de Antropología y Pensamiento Latinoamericano, 3 de Febrero 1370 (1426), Ciudad Autónoma de Buenos Aires, C1426BJN CABA
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Adam Mickiewicz University in Poznań
Affiliation as printed
Department of Computational Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznanskiego 6, Poznań, Wielkopolska, 61-614
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Affiliation as printed
Center for Evolutionary Hologenomics, Globe Institute, Københavns Universitet, ester Voldgade 44747, Copenhagen, Copenhagen K, 1350
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Queensland University of Technology
Affiliation as printed
Defence Genomics, Centre for Genomics and Personalised Health, Queensland University of Technology, Musk Ave 60, Kelvin Grove, Queensland, 4059
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Affiliation as printed
Department of Human Genetics, The University of Chicago, E. 58th St. 920, Chicago, Illinois, 60637
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Affiliation as printed
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
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Harvard University · Max Planck Institute for Evolutionary Anthropology · Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI) · Friedrich Schiller University Jena
Affiliation as printed
Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745
Department of Anthropology, Harvard University, Divinity Avenue 11, Cambridge, Massachusetts, 02138
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
Faculty of Biological Sciences, Institute of Microbiology, Friedrich-Schiller-Universität Jena, Neugasse 25, Jena, Thuringia, 07743
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Max Planck Institute for Evolutionary Anthropology · Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Knöll-Institut (HKI)
Affiliation as printed
Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745
Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Pl. 6, Leipzig, Saxony, 04103
Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Adolf-Reichwein-Straße 23, Jena, Thuringia, 07745
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