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

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.

Keywords: FAIR data; aDNA; environmental; metadata; metagenomics; microbial; microbiome; palaeogenomics.

Figure 1.. Growth of studies curated in the AncientMetagenomeDir as of v24.03.

(a) Number of ancient metagenomic publications published per year with open sequencing data and included in AncientMetagenomeDir. The original AncientMetagenomeDir publication was in 2020. (b) Cumulative sum of the number of published samples with publicly accessible sequencing data. (c) Cumulative sum of the number of ancient metagenomic sequencing data accessions of the samples in panel b. Data from Fellows Yates et al.

Figure 2.. Updated workflow for submission to AncientMetagenomeDir using the AMDirT autofill functionality.

The AncientMetagenomeDir submission workflow, as updated since. The general workflow remains the same, with issue creation for publication proposals, metadata submission by contributors via a branch and pull request, something that undergoes automated validation (with AMDirT validate), and later peer-review by AncientMetagenomeDir curators. The new addition is the use of autofill that is called via a GitHub Actions ‘bot’. This generates and uploads to the pull request in a comment a partially completed library metadata table that can be filled in, reviewed for accuracy and appended to the corresponding AncientMetagenomeDir library table as a part of the original sample pull request.

Figure 3.. Example workflow of using AMDirT viewer.

(a) The viewer opens in a user’s web browser, where the desired AncientMetagenomeDir version and table is selected. (b) Interaction with columns follows standard operations common to most spreadsheet software. Samples for download are selected using checkboxes. (c) The same interface can be used for the subsequent library metadata filter table. (d) After pressing ‘Validate library selection’, buttons appear for downloading various download scripts, reference, and pipeline input sheets.