This is the Supplemental Software package to the manuscript "Towards the biogeography of prokaryotic genes" by Coelho et al.:
Coelho, L.P., Alves, R., del Río, Á.R. et al. Towards the biogeography of prokaryotic genes. Nature 601, 252–256 (2022). https://doi.org/10.1038/s41586-021-04233-4
The purpose of this repository is to archive the code that generated both the resource and the analyses in the manuscript.
The Global Microbial Gene Catalogue is available at https://gmgc.embl.de.
The initial processing of the metagenomes is performed with NGLess, using MEGAHIT. ORF calling was performed using MetaGeneMark.
The catalog building was performed with a mixture of custom Haskell/C++ code and mmseqs2.
The subsquent analyses were performed in Python, using NumPy, Pandas, and Jug.
License: MIT
Sequence data: The full raw data (metagenomes) is available from ENA (see Supplemental Table 1 in the manuscript for a comprehensive list of all accession numbers.
Gene catalog & annotations: The gene catalog and its annotations is available at https://gmgc.embl.de.
Preprocessed data: For convenience, preprocessed derived data is also
available under the preprocessed/ directory. These were computed with the
code