For construction of the Escherichia reference database, all complete Escherichia genomes available in NCBI RefSeq were downloaded in July 2019 (929 genomes total; Additional file 2). All tools required to construct the StrainGST database are included in the StrainGE suite (kmer counting, clustering, and database construction). The full database with 361 Escherichia genomes uses 7.3 Gb of disk space.
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