This download contains an assembly nucleotide file representing the reference genome database used for HMP WGS read mapping, comprised of all archaeal, bacterial, lower eukaryote and viral organisms available in GenBank as of 11/2009. This includes reference genomes sequenced as part of the HMP initiative, as well as all other publicly available human associated reference genomes.

The database contains 131 archaeal strains over 97 species, 326 lower eukaryotes over 326 species, 3683 viral strains over 1420 species, and 1751 bacterial strains over 1253 species. The bacterial component of the database underwent a process of removing highly redundant, non HMP-sequenced reference genomes.

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