1. Class 02: Whole genome sequencing

2. The seminal papers www.cs.arizona.edu/people/gene/#papers ``Is Whole Genome Sequencing Feasible?'' ``Whole-Genome DNA Sequencing'' ``A Whole-Genome Assembly of Drosophila''``A Whole-Genome Assembly of Drosophila''

3. Shotgun sequencing Multiply target sequence Break sequences into random fragments Sort by size, discard big and small pieces ‘Insert into bacterial virus (‘vector’) Infect bacterial, and let it reproduce, ‘cloning’ the insert ‘Read’ the insert

4. Definitions G – length of target sequence L – avg length of read R – number of sequencing reads N – base pairs sequences = RL I – avg length of clone inset c – N/G = avg sequence coverage m – RI/2G, avg clone or map coverage

5. Problems Incomplete coverage Sequencing errors (<.01, avg) Unknown orientation Repeated sequences

6. Repeat problem Repeats vary in length, number, fidelity Length: few bp to thousands Number: highly variable, even by individual Fidelity: sometimes 1-2% variation, or less (multiple copies, pseudogenes) Long, infrequent, hi-fi repeats are the biggest problem

7. Overlap phase Compare every read (in both orientations) to every other Accept weighted agreement, bounded by fixed epsilon Exact solution is tractable Result is overlap graph, with each read a node, each overlap an edge

8. Layout phase Determine pairs which position each fragment In graph theoretic terms, find a spanning forest Optimal spanning forest is NP-hard Variation on greedy is commonly used

9. Consensus phase Problem: find consensus of multiple alignment of reads Initially, use overlaps in the spanning forest Apply one of several algorithms to refine this

10. Mates & contigs

11. ‘Double-barreled’ shotgun Choose inserts of length at least two ‘reads’ Sequence both ends (we know their relative orientation and distance) Used to order and orient contigs Use a supplementary process to fill in the gaps between contigs

12. Clone by clone (HGP)

13. Whole genome assembly Mates can resolve short repeats Problem when you ‘exit’ the repeat: you don’t know which is right Resolve using a mate pair which has a read in the unique flanking sequence

14. Whole genome (illustr)