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8	Whole Genome Sequencing (WGS)
9	WGS sequencing: fragments We start with millions of pairs of reads, 100 - 1000 bases each Multiple copies of DNA provide multiple coverage by reads The problem of genome assembly is to recover the original sequence of bases of the genome (as much as possible…).
10	Assembling a jigsaw puzzle 1 The task of the assembly becomes the task of assembling a giant jigsaw puzzle We look for reads whose sequences suggest that they came from the same place in the genome: AGTGATTAGATGATAGTAGA         |||||||||         GATGATAGTAGAGGATAGATTTA
11	Assembling a jigsaw puzzle 2 Then we put “overlapping” reads together AGTGATTAGATGATAGTAGA        AGATGATAGTAGAGATAGATAGACC                      ATAGATAGACCACTCATCATAC AGTGATTAGATGATAGTAGAGATAGATAGACCACTCATCATAC
12	Assembling a jigsaw puzzle 3 We use read pairing information to order and orient contigs to produce scaffolds – the final product of assembly
13	Difficulties in NGS assembly
14	Repeat regions may cause omissions
15	Erroneous duplications Two recent published assemblies of the cow genome: UMD2 and BosTau4 Segmental duplications were a central theme in BosTau4 genome paper UMD2 assembly had many fewer duplications We examined the duplications, > 99.5% identity, >5000bp, one copy in the UMD2 assembly and two copies in the BosTau4
16	Next Gen vs. Sanger Sequencing
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