Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT - Institut Pasteur Accéder directement au contenu
Article Dans Une Revue F1000Research Année : 2023

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

1 Leibniz Institute for Natural Product Research and Infection Biology (Hans Knoell Institute)
2 Max Planck Institute for Evolutionary Anthropology [Leipzig]
3 Uppsala Universitet [Uppsala]
4 Unipd - Università degli Studi di Padova = University of Padua
5 UCPH - University of Copenhagen = Københavns Universitet
6 University of York [York, UK]
7 Max Planck Institute of Geoanthropology
8 Universiteit Leiden = Leiden University
9 Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany]
10 Paléogénomique microbienne - Microbial paleogenomics
11 Harvard University
12 MPIIB - Max Planck Institute for Infection Biology
13 NUI Galway - National University of Ireland [Galway]
14 Trinity College Dublin
15 ULL - Universidad de La Laguna [Tenerife - SP]
16 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
17 Wageningen Environmental Research (Alterra)
18 Universiteit Utrecht
19 ASU - Arizona State University [Tempe]
20 Durham University
21 Edin. - University of Edinburgh
22 University of Otago [Dunedin, Nouvelle-Zélande]
23 UNAM - Universidad Nacional Autónoma de México = National Autonomous University of Mexico
24 EURAC - European Academy Bozen/Bolzano
25 UNITN - Università degli Studi di Trento = University of Trento
26 TAU - Tel Aviv University
27 Science for Life Laboratory [Solna]
28 Lund University
29 University of Texas at Austin [Austin]
30 INAPL - Instituto Nacional de Antropología y Pensamiento Latinoamericano [Buenos Aires]
31 CAGT - Centre d'anthropologie et de génomique de Toulouse
32 UAM - Uniwersytet im. Adama Mickiewicza w Poznaniu = Adam Mickiewicz University in Poznań
33 QUT - Queensland University of Technology [Brisbane]
34 University of Chicago
I-Ting Huang
  • Fonction : Auteur
Shreya L Ramachandran

Résumé

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.github.io) 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 automated metadata curation and data validation, as well as rapid data filtering and downloading. Results : AncientMetagenomeDir was extended to include standardised metadata of over 5000 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 and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.
Fichier principal
Vignette du fichier
3cd9ab38-2281-435b-9928-95b81ef8100b_134798_-_james_fellows_yates.pdf (3.89 Mo) Télécharger le fichier
Origine : Publication financée par une institution
Licence : CC BY - Paternité

Dates et versions

pasteur-04261820 , version 1 (27-10-2023)

Licence

Paternité

Identifiants

Citer

Maxime Borry, Adrian Forsythe, Aida Andrades Valtueña, Alexander Hübner, Anan Ibrahim, et al.. Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT. F1000Research, 2023, 12, pp.926. ⟨10.12688/f1000research.134798.1⟩. ⟨pasteur-04261820⟩
28 Consultations
5 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More