Kalanchoe

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Revision as of 05:55, 9 February 2011 by Dpuiu (talk | contribs)
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Data

  • ~5x 454 from a variety of library sizes


  • ~20x illumina.
  • Location:
 /fs/szattic-asmg7/Kalenchoe_genome/

Assembly

Blogs

 assemble the illumina lane with SOAPdenovo and then 
 assemble with newbler the 454 lanes and the resulting contig of SOAP2.  
 SOAP uses a de bruijn graph data structure that is well suited for short illumina reads but it is not enough flexible in order to handle 454 reads.
 Newbler, instead, is based on Overlap Layout Approach that work well with long reads
  • CABOG ... throws a lot of errors on our architecture for some reason
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