ToRQuEMaDA: Tool for retrieving queried eubacteria, metadata and dereplicating assemblie

The fast-growing number of available prokaryotic genomes, along with their uneven taxonomic distribution, is a problem when trying to assemble broadly sampled genome sets for phylogenomics and comparative genomics. Indeed, most of the new genomes belong to the same subset of hyper-sampled phyla, such as Proteobacteria and Firmicutes, or even to single species, such as Escherichia coli (>3000 genomes as of March 2017), while the continuous flow of newly discovered phyla prompts for regular updates of in-house databases. This situation makes it difficult to maintain sets of representative genomes combining lesser known phyla, for which only few species are available, and sound subsets of highly abundant phyla. An automated method is required but none are publicly available. In this work, the kmer composition of DNA sequences, in conjunction with quality metrics for publicly available assemblies, was used to develop an automated approach for selecting a high-quality subset of
representative genomes without redundancy by using our hybrid divide-and-conquer / greedy clustering method.