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SUMMARY:NGS Sequence Assembly for Metagenomic Data - Chin\, F (University 
 of Hong Kong)
DTSTART:20140325T161500Z
DTEND:20140325T170000Z
UID:TALK51608@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Next-generation sequencing techniques allow us to generate rea
 ds from a microbial environment in order to analyze the microbial communit
 y. However\, assembling of a set of mixed reads from thousands of differen
 t species to form contigs is a bottleneck of metagenomic research. Althoug
 h there are many assemblers for assembling reads sampled from a single gen
 ome\, only a few assemblers work on metagenomic data. Moreover\, the perfo
 rmances of these assemblers on metagenomic data are far from satisfactory 
 because of the following reasons: (1) up to 99% of the species in the samp
 le are unknown and have no reference genomes\, (2) sequencing depths of ge
 nomes from different species are highly uneven because different species i
 n a sample have different abundances (over 100 times)\, and (3) genomes of
  subspecies and species in a sample can be very similar and the existence 
 of common regions across different genomes make the assembly problem much 
 more complicated. In this talk\, different techniques (IDBA-UD and MetaIDB
 A)\, with possible incorporation with binning results (MetaCluster)\, for 
 solving these three problems will be presented. \nAs the last two problems
  are more severe for RNA-Seq data from metagenomic sample (metatranscripto
 mic data) than metagenomic data\, no existing assemblers work well on the 
 metatranscriptome data (even though gene sequence information of some micr
 obes might be known).  Main features of a metatranscriptome assembler (IDB
 A-MT) will also be discussed.\n
LOCATION:Seminar Room 1\, Newton Institute
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