2014.03.31.GenomeAccess.Sequencing and Assembly

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SV Types • Different structural variation types / misassemblies will be apparent by their pattern of breakpoints • Most breakpoints will be at or near repeats • Things quickly get complicated in real genomes http://mummer.sf.net/manual/ AlignmentTypes.pdf
Seed-<strong>and</strong>-extend with MUMmer How can quickly align two genomes? 1. Find maximal-unique-matches (MUMs) w Match: exact match of a minimum length w Maximal: cannot be extended in either direction without a mismatch w Unique w occurs only once in both sequences (MUM) w occurs only once in a single sequence (MAM) w occurs one or more times in either sequence (MEM) 2. Cluster MUMs w using size, gap <strong>and</strong> distance parameters 3. Extend clusters w using modified Smith-Waterman algorithm
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 and 24: Coverage and Read Length Idealized
Page 25 and 26: Errors in the graph Clip Tips Pop B
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: B Translocation Inversion Insertion
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

2014.03.31.GenomeAccess.Sequencing and Assembly

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