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SUMMARY:Metagenomic assembly and characterisation of viral signatures with
  MetaCortex - Leggett\, R (The Genome Analysis Centre (TGAC))
DTSTART:20140325T114500Z
DTEND:20140325T123000Z
UID:TALK51610@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Co-authors: Ricardo Ramirez Gonzalez (The Genome Analysis Cent
 re (TGAC))\, Kate Baker (Wellcome Trust Sanger Institute)\, Pablo Murcia (
 MRC-University of Glasgow Centre for Virus Research)\, Mario Caccamo (The 
 Genome Analysis Centre (TGAC)) \n\nMost standard tools for assembly of nex
 t generation sequencing reads are not designed for metagenomic datasets\, 
 rather the aim is to assemble a single genome into a relatively small numb
 er of large contigs or scaffolds. In part this is achieved by implementati
 on of algorithms designed to remove sequencing errors and to smooth small 
 variations that would otherwise break contiguity. However\, this approach 
 has limits when used to analyse environmental samples\, in which fragments
  of DNA from multiple organisms may be present and where the aim is not to
  assemble a single genome\, but to understand the wider biological composi
 tion of the sample. \n\nThe last 2 years has seen the emergence of a numbe
 r of specialised metagenomic assemblers aimed at addressing this tools gap
 . One example of this is our own work\, MetaCortex\, which is capable of a
 ssembling sequencing reads and outputting contigs indicative of the entire
  set of organisms present in a sample. MetaCortex works by identifying sub
 -graphs within the wider de Bruijn graph assembly and building contigs\, w
 hich represent the consensus path through these components. In doing so\, 
 variation information is preserved and it is possible to detect organisms 
 present in the sample with low read coverage. We applied this method to th
 e analysis of DNA samples from Eidolon helvum\, a species of bat implicate
 d in the transmission of zoonotic disease to humans and were able to ident
 ify hundreds of different viral DNA signatures within samples.\n
LOCATION:Seminar Room 1\, Newton Institute
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