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picture1_Pyrosequencing Slideshare 66776 | Saahpc12 Talk


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File: Pyrosequencing Slideshare 66776 | Saahpc12 Talk
agenda background needleman wunsch gpu implementation optimization steps results symposium on application accelerators in high performance computing 2 roche 454 gs flx titanium xl typical throughput 700 mb run time ...

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                          Agenda
    • Background
    • Needleman-Wunsch
    • GPU Implementation
    • Optimization steps
    • Results
                    Symposium on Application Accelerators in High-Performance Computing  2
                               Roche 454
   GS FLX Titanium XL+
   Typical Throughput     700 Mb
   Run Time               23 hours
   Read Length            Up to 1,000 bp
   Reads per Run          ~1,000,000 shotgun
                          Symposium on Application Accelerators in High-Performance Computing  3
           From Genomics to Metagenomics
                    Symposium on Application Accelerators in High-Performance Computing  4
                        Why AmpliconNoise?
 454 Pyrosequencing in Metagenomics has 
 no consensus sequences
            --------
 Overestimation of the number of 
 operational taxonomic units (OTUs) 
                C. Quince, A. Lanzn, T. Curtis, R. Davenport, N. Hall,I. Head, L.Read, and W. Sloan, “Accurate 
                determination of microbial diversity from 454 pyrosequencing data,” Nature Methods, vol. 6, no. 9, pp. 
                639–641, 2009.
                           Symposium on Application Accelerators in High-Performance Computing  5
                                  SeqDist
     •  Clustering method to “merge” the sequences with minor differences
     •  SeqDist
         – How to define the distance between two potential sequences?
         – Pairwise Needleman-Wunsch and Why?
        short sequences number         Sequence Alignment Between two 
           1 2 3 4 5 6 … n             short sequences
         1 - C C C C C C C            sequence 1:   A G G T C C A G C A T
                       c
         2 - - C C C C C C            sequence 2:   A C C T A G C C A A T
         3 - - - C C C C C
         4 - - - - C C C C
         5 - - - - - C C C
         6 - - - - - - C C
         …- - - - - - - C          C:  Sequences Distance 
                                   Computation
         n - - - - - - - -
                          Symposium on Application Accelerators in High-Performance Computing  6
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...Agenda background needleman wunsch gpu implementation optimization steps results symposium on application accelerators in high performance computing roche gs flx titanium xl typical throughput mb run time hours read length up to bp reads per shotgun from genomics metagenomics why ampliconnoise pyrosequencing has no consensus sequences overestimation of the number operational taxonomic units otus c quince a lanzn t curtis r davenport n hall i head l and w sloan accurate determination microbial diversity data nature methods vol pp seqdist clustering method merge with minor differences how define distance between two potential pairwise short sequence alignment g computation...

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