Agenda
    • Background
    • Next Generation Sequencing
    • Sequence Assembly
    • Sequence Alignment
    • Traditional Alignment Algorithms
    • Next Generation Alignment Algorithms
    • Conclusion
                             Andy Nagar                   2
                        Background
   • Earlier sequencing methods were based on Sanger 
      sequencing, which goes back to the 1970s.
   • Sequencing was slow, bases were read one at a time.
   • Separation is done by
      electrophoresis.
   • Readout by fluorescent tags.
                              Andy Nagar                    3
                                                      Source:[Wikipedia]
                          Background
   • To complete second generation genome projects such 
      as the Human Genome Project, need for faster and 
      high-throughput sequencing.
   • Next-Generation Sequencing technologies based on 
      various implementations of cyclic array sequencing.
   • Cyclic Array Sequencing is based on the idea of 
      sequencing of an array of DNA features by continuous 
      process of enzymatic separation and imaging-based 
      data collection. 
                                Andy Nagar                       4
                  Growth in Sequencing
                               Growth of Next - Gen
                               Sequencing – doubles every month
                            Andy Nagar                  5
                                                       Source:[6]
                Next Generation Sequencing
    • Workflow :
     •DNA is fragmented
     •Adaptors ligated to fragments
     •Several possible protocols 
     yield array of PCR colonies.
     •Enyzmatic extension with 
     fluorescently tagged 
     nucleotides.
     •Cyclic readout by imaging the 
     array.
                                  Andy Nagar                         6
                                                                   Source:[10]