Metagenomics Sensitive and Accurate Taxa Classification Ebrahim Afshinnekoo MetaSUB Global Project Director Mason Lab Weill Cornell Medical College June 20 th 2015 nycpathomap ID: 524371
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The Grand Challenge in
MetagenomicsSensitive and Accurate Taxa Classification
Ebrahim AfshinnekooMetaSUB Global Project DirectorMason Lab Weill Cornell Medical CollegeJune 20th, 2015
@nycpathomapSlide2Slide3Slide4
But what about everything else…?Slide5
We’re only as good as our databases…
…and there is a great need for standards!Slide6
Nucleic Acids
Research Group
More coming from the Metagenomics Research Group –stay tuned! Slide7Slide8
Comparing the tools…Slide9
The “Holy Grail” in Metagenomics
One Tool to rule them allOne Tool to find the taxaOne Tool to bring relative abundancesAnd in the metagenomics bind themSlide10
A more integrative approach…Slide11Slide12Slide13
http://
microbe.net/2015/02/17/the-long-road-from-data-to-wisdom-and-from-
dna-to-pathogen/Slide14
B.
anthracis found by Kraken, MetaPhlAn, SURPI, BWA, PhyloSift. But scant pXO, no
PlcR SNP.Thus, no evidence of a pathogen in the subway.http://read-lab-confederation.github.io/nyc-subway-anthrax-study/Slide15
https://github.com/poeli/GOTTCHA
Slide16
Great name, sounds good, I wonder what it’ll find in some samples…Slide17Slide18Slide19Slide20
Conclusion:
The “G” in GOTTCHA actually stands for GonorrheaSlide21
MetaSUB Goals
StandardsExpand the DatabaseIntegrative taxa classification pipeline
- Focus on responsible interpretation!(4) Expand the analysisMBQCSlide22
Thanks to the Swabbing Teams! www.pathomap.org/people/