Species and its subspecies/strain both appear in the centrifuge report

[zifanzhu]

Hi there,

I'm using centrifuge (v1.0.4-beta) to perform taxonomic profiling of a shotgun sequencing data. Here is a part of the report file I got:

We see from the highlighted part that both species Lactococcus lactis and its subspecies appear in the report and get nonzero abundance. This makes me confused. From my understanding, reads mapped to a subspecies/strain could also be mapped to its corresponding species; thus, one should either group subspecies/strain abundance into its species or set species abundance to 0 and only keep its various subspecies/strain abundances. I wonder if there is any overlap in the abundances of Lactococcus lactis and its subspecies.

Really appreciate it if anyone can help!

Best, Zifan

[mourisl]

Sorry for the late reply, Centrifuge does not group the abundances from sub species.

[zifanzhu]

Thanks for your reply!