On 2013 Oct 23, Stephen Turner commented:

This paper presents a new method for species identification and strain attribution using next-generation sequencing data from a cultured pathogen or mixed environmental sample. The paper presented compelling results showing that this new method performed markedly better than a 'naive' mapping approach and other leading read classification methods based on taxonomic binning or compositional analysis. Importantly, the method was shown to work well, even when the species being sequenced was not present in the reference database; sequence data from this organism were assigned to the closest phylogenetic near-neighbor. Finally, the method was also shown to work well when multiple species were present, faithfully recapitulating the actual abundances of organisms present in the sample.

On 2013 Oct 23, Stephen Turner commented:

This paper presents a new method for species identification and strain attribution using next-generation sequencing data from a cultured pathogen or mixed environmental sample. The paper presented compelling results showing that this new method performed markedly better than a 'naive' mapping approach and other leading read classification methods based on taxonomic binning or compositional analysis. Importantly, the method was shown to work well, even when the species being sequenced was not present in the reference database; sequence data from this organism were assigned to the closest phylogenetic near-neighbor. Finally, the method was also shown to work well when multiple species were present, faithfully recapitulating the actual abundances of organisms present in the sample.