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SUMMARY:Species identification from medical metagenomic sequence data - Iq
 bal\, Z (University of Oxford)
DTSTART:20140325T153000Z
DTEND:20140325T161500Z
UID:TALK51612@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Species identification from metagenomic sequence data has attr
 acted considerable attention recently\, and a number of software solutions
  are now available\, based on whoe-genome assemblies\, mapping to referenc
 es\, or informative kmers. In this talk I focus on a small corner of this 
 area\, that of species identification from medical samples\, where we have
  an idea from the patient's condition (and perhaps from inspection of cult
 ure) what genus of bacterium we expect to find\, but we do not know if the
 re is a mixture. I specifically look at the case of Staphylococcus aureus\
 , a commensal organism which lives in the noses of ~30% of us\, and yet wh
 ich can be a pathogen. Many assemblies of S. aureus strains are present\, 
 but generally only one assembly per species for other Staphylococcus speci
 es (some of which can cause illness). I'll talk about how we can address t
 he issues which arise when we want confident answers in the face of such a
  biased set of prior information. \n
LOCATION:Seminar Room 1\, Newton Institute
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