Associating environmental metadata with microbial genomes retrieved from metagenomes is a notoriously hard problem. Metadata for the source sample(s) is often limited, and can be hard to retrieve at scale. We circumvented this problem by using the detection of GlobDB genomes in the 700k+ metagenomes present in the Sandpiper database, created using SingleM by Ben Woodcroft and colleagues.

We are very happy to announce the first release of the the amino acid sequence toolkit (AASTK). 

AASTK is a suite of tools designed to leverage the genomic diversity captured by the GlobDB to create and analyze datasets of homologous proteins. Current functionality of AASTK includes tree-of-life scale dataset building, curation, and maintenance, as well as clustering of protein datasets, genomic context analysis, and metadata retrieval. 

The r232 release of the GlobDB is in preparation, and will be based on the upcoming GTDB release. The existing data sources in the GlobDB will be dereplicated against the new GTDB release. In addition, we will include genomes from the data sources listed below if they represent species that aren't present in the INSDC databases or previous GlobDB releases.

If you have suggestions for additional data sources to include, please contact Daan Speth. 

On Wednesday February 18th the Life Science Compute Cluster (LiSC) that hosts the GlobDB will be shut off for maintenance. This means no downloads will be possible that day (at least during European day time). If all goes well, LiSC will be back up the next day.