2014.03.31.GenomeAccess.Sequencing and Assembly

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Errors Unitigging / Unipathing • After simplification <strong>and</strong> correction, compress graph down to its non-branching initial contigs – Aka “unitigs”, “unipaths” – Unitigs end because of (1) lack of coverage, (2) errors, <strong>and</strong> (3) repeats
Errors in the graph Clip Tips Pop Bubbles was the worst of times, was the worst of tymes, the worst of times, it was the worst of times, was the worst of tymes, times, it was the age tymes, it was the age the worst of tymes, tymes, was the worst of the worst of times, was the worst of times, it was the age worst of times, it (Chaisson, 2009)
Page 1 and 2: Genome Sequencing & Assembly Michae
Page 3 and 4: Outline 1. Assembly theory 1. Assem
Page 5 and 6: It was the best of age of wisdom, i
Page 7 and 8: It was the best de Bruijn Graph Ass
Page 9 and 10: The full tale … it was the best o
Page 11 and 12: Assembly Complexity A R B R C
Page 13 and 14: • Novel genomes Assembly Applicat
Page 15 and 16: Why are genomes hard to assemble? 1
Page 17 and 18: Illumina Sequencing by Synthesis 1.
Page 19 and 20: Balls in Bins 1x
Page 21 and 22: Balls in Bins 4x
Page 23: Coverage and Read Length Idealized
Page 27 and 28: Repeats and Coverage A-stat Statist
Page 29 and 30: Scaffolding • Initial contigs (ak
Page 31 and 32: Break
Page 33 and 34: Whole Genome Alignment with MUMmer
Page 35 and 36: Not so fast... • Genome A may hav
Page 37 and 38: B Translocation Inversion Insertion
Page 39 and 40: Seed-and-extend with MUMmer How can
Page 42 and 43: Outline 1. Assembly theory 1. Assem
Page 44 and 45: How ALLPATHS-LG works reads correct
Page 46 and 47: Error correction Given a crystal ba
Page 48 and 49: Read doubling To close a read pair
Page 50 and 51: Localization I. Find ‘seed’ uni
Page 52 and 53: Large genome recipe: ALLPATHS-LG vs
Page 54 and 55: Genome assembly with the Celera Ass
Page 56 and 57: Hybrid Sequencing Illumina Sequenci
Page 58 and 59: SMRT Sequencing Data TTGTAAGCAGTTGA
Page 60 and 61: PacBio Assembly Algorithms PBJelly
Page 62 and 63: S. cerevisiae W303 S288C Reference
Page 64 and 65: A. thaliana Ler-0 http://blog.pacif
Page 66 and 67: A. thaliana Ler-0 http://blog.pacif
Page 68 and 69: O. sativa pv Indica (IR64) Genome s
Page 70 and 71: Assembly Complexity of Long Reads S
Page 72 and 73: Assembly Complexity of Long Reads S
Page 74 and 75:
Assembly Summary Assembly quality d
Page 76:
Thank You! http://schatzlab.cshl.ed
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2014.03.31.GenomeAccess.Sequencing and Assembly

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