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CATEGORIES:Isaac Newton Institute Seminar Series
SUMMARY:Quikr: Rapid Bacterial Community Reconstruction Vi
a Compressive Sensing - Koslicki\, D (Oregon State
University)
DTSTART;TZID=Europe/London:20140327T134500
DTEND;TZID=Europe/London:20140327T141500
UID:TALK51657AThttp://talks.cam.ac.uk
URL:http://talks.cam.ac.uk/talk/index/51657
DESCRIPTION:Co-authors: Simon Foucart (University of Georgia)\
, Gail Rosen (Drexel University) \n\nMany metageno
mic studies compare hundreds to thousands of envir
onmental and health-related samples by extracting
and sequencing their DNA. However\, one of the fir
st steps - to determine what bacteria are actually
in the sample - can be a computationally time-con
suming task since most methods rely on computing t
he classification of each individual read out of t
ens to hundreds of thousands of reads. We introduc
e Quikr: a QUadratic\, K-mer based\, Iterative\, R
econstruction method which computes a vector of ta
xonomic assignments and their proportions in the s
ample using an optimization technique motivated fr
om the mathematical theory of compressive sensing.
On both simulated and actual biological data\, we
demonstrate that Quikr is typically more accurate
as well as typically orders of magnitude faster t
han the most commonly utilized taxonomic assignmen
t techniques for both whole genome techniques (Met
aphyler\, Metaphlan) and 16S rRNA techniques (the
Ribosomal Database Project's Naive Bayesian Classi
fier). We also show that in general nonnegative L1
minimization can be reduced to a simple nonnegati
ve least squares problem.\n\nRelated Links: \nhttp
://www.math.uga.edu/~foucart/WGSQuikr_final.pdf -
WGSQuikr preprint \n\nhttp://www.math.uga.edu/~fou
cart/QuikrRevisionPrePrint.pdf - Quikr preprint \n
\nhttp://www.math.uga.edu/~foucart/SRasNNLS_final.
pdf - Sparse recovery by means of nonnegative leas
t squares \n
LOCATION:Seminar Room 1\, Newton Institute
CONTACT:Mustapha Amrani
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