Our Mtb DNA on the Tapestation
     MinION fastq file
                2 records – 576 bp; 1316 bp
     Illumina fastq file
                   all records ~100 bp
               There are 3 main approaches to 
                                           sequencing
                           Market           Approach / USP       Read      Achievements    Ideal for:
                           dominance                             length
             st
            1  Generation  Applied          Sequencing by        1 kb      Most primary    PCR products 
            (Sanger)       Biosystems       synthesis (SBS)                drafts, e.g.    (genotyping)
                                            - Low throughput               Mtb, human
             nd
            2              Illumina         SBS                  100 bp    Cheap, rapid    WGS
            Generation     (IonTorrent)     - Massively parallel           resequencing 
                                            - Very high                    of millions of 
                                            throughput                     genomes
             rd
            3              Oxford           Single molecule      100 bp –  Sequencing in   Real-time 
            Generation     Nanopore         sequencing (SMS)     500 Mbp field / very      sequencing
                           (PacBio)                                        long lengths
           All genomes are ‘assembled’ by piecing together 
         small fragments into a consensus (‘shotgun sequencing’)
     GGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTG
     GGCACCAGCCAGCTGAGCCAATTCATGGACCAGTACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTG 
     GGCACCAGCCAGCTGAGCCCATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTG 
     GGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTG 
     GGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTG
     GGCACCAGCCAGCTGAGCCAATTCATGGACCAGAACAACCCGCTGTCGGGGTTGACCCACAAGCGCCGACTGTCGGCGCTG 
     Consensus
      •  The first full assembly of any genome from scratch (de novo) and its annotation is hard
      •  It’s a hypothesis of a genome at a moment in time
      •  Overlapping sequences extends consensus, and improves evidence for each base call
      •  Errors occur for many reasons