A curated data resource of 214K metagenomes for characterization of the global resistome

Data files of the curated resource of 214K metagenomes for characterization of the global resistome.

We have retrieved 214K metagenomic samples and now share the results here on Zenodo of our large-scale read mapping effort.

There are five tables uploaded in three formats (TSV, HDF and MySQL dump):

• metadata.* : contains metadata for all sequencing runs.
• ARG.* : contain read alignment counts of antimicrobial resistance genes (ARGs).
• rRNA.* : contain read alignment counts of 16S/18S rRNA genes.¹
• diversity.* : contain diversity measures for ARGs and two taxonomic groups of rRNA genes (phylum, genus).
• ResFinder_anno.* : contain sequence information on the different ARGs, such as gene_lengths, resistance class, etc.

Note that the HDF file rRNA.h5 is split into batches of 10,000 rows. To load it, the keys are in the format of "table_{i}", where i=0,1,2,..,4736

Details on the different tables are available at https://hmmartiny.github.io/mARG/

Additionaly, we have shared the data used to create the figures in the manuscript in the ZIP file named "figure_data.zip".

Any further questions or issues, please contact H.-M. Martiny at hanmar@food.dtu.dk