Overview of Genome Assembly Algorithms
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The document discusses genome assembly algorithms and software, specifically focusing on Overlap-Layout-Consensus (OLC) and De Bruijn graph methods. It highlights the challenges and methodologies involved in reconstructing genomes from sequencer reads and provides an overview of various assembly software like Celera Assembler and Velvet. Additionally, it touches on the underlying graph theory concepts that facilitate genome assembly, including the construction and traversal of assembly graphs.
Overview of Genome Assembly Algorithms
- 1. Introduction OLC Graph theory and assembly deBruijn - Euler Genome Assembly Algorithms and Software (or...what to do with all that sequence data ?) Konstantinos Krampis Asst. Professor, Informatics J. Craig Venter Institute George Washington University, Nov. 2nd 2011 Konstantinos Krampis Genome Assembly Algorithms and Software
- 2. Introduction OLC Graph theory and assembly deBruijn - Euler Introduction Why do we need genome assembly Definitions of genome assembly OLC Overlap Layout Consensus OLC assembly software and publications Graph theory and assembly Definition of a graph Graphs and genome assembly deBruijn - Euler An alternative assembly graph Constructing a de Bruijn graph from reads Genome assembly from de Bruijn graphs deBruijn assembly software and publications Konstantinos Krampis Genome Assembly Algorithms and Software
- 3. Introduction OLC Why do we need genome assembly Graph theory and assembly Definitions of genome assembly deBruijn - Euler Cannot read the complete genome with the sequencer from one end to the other ! DNA isolated from a cell is amplified Broken into fragments (shearing) Fragments are ”read” with the sequencer Use the fragments - reads to reconstruct the genome from Credit: Masahiro Kasahara, Large-Scale Genome Sequence sequencing reads Processing, Imprerial College Press Konstantinos Krampis Genome Assembly Algorithms and Software
- 4. Introduction OLC Why do we need genome assembly Graph theory and assembly Definitions of genome assembly deBruijn - Euler Assembly: hierarchical process to reconstruct genome from reads Assemble the puzzle of the genome from the reads: overlaps connect the pieces Oversample the genome so that reads overlap Key approach: data structure representing overlaps, and algorithms operating on that Credit: Masahiro Kasahara, Large-Scale Genome Sequence data structure Processing, Imprerial College Press Konstantinos Krampis Genome Assembly Algorithms and Software
- 5. Introduction OLC Why do we need genome assembly Graph theory and assembly Definitions of genome assembly deBruijn - Euler Two major algorithmic paradigms for genome assembly Overlap - Layout - Consensus (OLC): well established, more powerful method, but more difficult to implement OLC: first to be used successfully for complex Eucaryotic genomes (Drosophila,H.sapiens) deBruijn - Euler: newer, easier to implement, problematic in complex genomes (for current implementations) Konstantinos Krampis Genome Assembly Algorithms and Software
- 6. Introduction Overlap OLC Layout Graph theory and assembly Consensus deBruijn - Euler OLC assembly software and publications Find Overlaps by aligning the sequence of the reads Layout the reads based on which aligns to which Get Consensus by joining all read sequences, merging overlaps Sequencer reads in random direction, left-to-right or Credit: Masahiro Kasahara, Large-Scale Genome Sequence Processing, right-to-left Imprerial College Press Konstantinos Krampis Genome Assembly Algorithms and Software
- 7. Introduction Overlap OLC Layout Graph theory and assembly Consensus deBruijn - Euler OLC assembly software and publications Sequence alignment, all-against-all reads (Smith-Watermann, BLAST, other?) Computationally intensive but easily parallelizable Represent read overlap by connecting with directed Credit: Kececioglu and Myers 1995, Algorithmica 13:7-51 link First step in creating the genome assembly graph (more later) Konstantinos Krampis Genome Assembly Algorithms and Software
- 8. Introduction Overlap OLC Layout Graph theory and assembly Consensus deBruijn - Euler OLC assembly software and publications Create a consistent linear (ideally) ordering of the reads Remove redundancy, so no two dovetails leave the same edge No containment edge is followed by a dovetail edge Remove cycles, one link in, one out Konstantinos Krampis Genome Assembly Algorithms and Software
- 9. Introduction Overlap OLC Layout Graph theory and assembly Consensus deBruijn - Euler OLC assembly software and publications Multiple Sequence Alignment (ClustalW) algorithms ? No phylogeny here... Vote for the most abundant nucleotide for each position Incorporate read quality data Create pre-consensus from high-quality reads, and align remaining reads to it Konstantinos Krampis Genome Assembly Algorithms and Software
- 10. Introduction Overlap OLC Layout Graph theory and assembly Consensus deBruijn - Euler OLC assembly software and publications Celera Assembler Developed at Celera Genomics for first Drosophila and human genome assemblies Continuoued development at J. Craig Venter Inst. as open source project http://wgs-assembler.SourceForge.net (Licence: GPL) Plently of wiki (developer + user) documentation, examples, user forums Other OLC implementations: Arachne, PCAP, Newbler, Phrap, TIGR Assembler Konstantinos Krampis Genome Assembly Algorithms and Software
- 11. Introduction Overlap OLC Layout Graph theory and assembly Consensus deBruijn - Euler OLC assembly software and publications Celera Assembler publications Myers et al (2000) A whole-genome assembly of Drosophila Levy et al (2007) The diploid genome sequence of an individual human Zimin et al (2009) The domestic cow, Bos taurus Dalloul et al (2010) The domestic turkey, Meleagris gallopavo Lorenzi et al (2010) New assembly of Entamoeba histolytica Lawniczak et al (2010) Divergence in Anopheles gambiae Jones et al (2011) The marine filamentous cyanobacterium Lyngbya majuscula Miller et al The Tasmanian devil, Sarcophilus harrisii Prfer et al The great ape bonobo, Pan paniscus Gordon et al The cotton bollworm moth, Helicoverpa Konstantinos Krampis Genome Assembly Algorithms and Software
- 12. Introduction OLC Definition of a graph Graph theory and assembly Graphs and genome assembly deBruijn - Euler and now a bit of Graph Theory... Konstantinos Krampis Genome Assembly Algorithms and Software
- 13. Introduction OLC Definition of a graph Graph theory and assembly Graphs and genome assembly deBruijn - Euler Graph G with set of vertices (nodes) V: {P,T,Q,S,R} set of edges (links between nodes) E: {(P,T),(P,Q),(P,S),(Q,T), (S,T),(Q,S),(S,Q),(Q,R),(R,S)} walk from P to R:(P,Q),(Q,R) walk from R to T:(R,S),(S,Q),(Q,T) or (R,S),(S,T) Credit: Introduction to Graph Theor Robert J. Wilson walk from R to P: not possible Konstantinos Krampis Genome Assembly Algorithms and Software
- 14. Introduction OLC Definition of a graph Graph theory and assembly Graphs and genome assembly deBruijn - Euler Trail: a walk of the graph where each edge is visited only once Example Trail: (P,Q), (Q,R), (R,S), (S,Q), (Q,S), (S,T) Path: a walk where each vertice is visited once Example Path: (P,Q), (Q,R), (R,S), (S,T) Konstantinos Krampis Genome Assembly Algorithms and Software
- 15. Introduction OLC Definition of a graph Graph theory and assembly Graphs and genome assembly deBruijn - Euler Credit: Saad Mneimneh, CUNY Konstantinos Krampis Genome Assembly Algorithms and Software
- 16. Introduction OLC Definition of a graph Graph theory and assembly Graphs and genome assembly deBruijn - Euler Represent sequence overlaps as a graph with weighted edges SCS solution: find Path (visit all edges and vertices once) that maximizes weight sum Hamiltonian Cycle or Traveling Saleman Problem Konstantinos Krampis Genome Assembly Algorithms and Software
- 17. Introduction OLC Definition of a graph Graph theory and assembly Graphs and genome assembly deBruijn - Euler Which edge to start from? NO: misses a vertex NO: misses edge with large weight Konstantinos Krampis Genome Assembly Algorithms and Software
- 18. Introduction OLC Definition of a graph Graph theory and assembly Graphs and genome assembly deBruijn - Euler YES!: all vertices and edge with large weight Konstantinos Krampis Genome Assembly Algorithms and Software
- 19. Introduction OLC Definition of a graph Graph theory and assembly Graphs and genome assembly deBruijn - Euler A more realistic version of a read / string overlap graph (C. jejuni) Credit: Eugene W. Myers Bioinformatics 21:79-85 Konstantinos Krampis Genome Assembly Algorithms and Software
- 20. Introduction OLC Definition of a graph Graph theory and assembly Graphs and genome assembly deBruijn - Euler Computational Complexity SCS solution by searching for a Hamiltonian Cycle on a graph is a difficult algorithmic problem (NP-hard) Using approximation or greedy algorithms can yield a 2 to 4-aprroximation solutions (twice or four times the length of the optimal-shortest string) Transformation of Overlap Graph to String Graph leads to Polynomial time solution. No Polynomial(P) : O(n), O(n2 ), O(n3 )etc. assembler implementation yet. (1) Konstantinos Krampis Genome Assembly Algorithms and Software
- 21. Introduction An alternative assembly graph OLC Constructing a de Bruijn graph from reads Graph theory and assembly Genome assembly from de Bruijn graphs deBruijn - Euler deBruijn assembly software and publications Pevzner, Tang and Waterman, An Eulerian path approach to DNA fragment assembly, PNAS 98 2001 9748-9753. Konstantinos Krampis Genome Assembly Algorithms and Software
- 22. Introduction An alternative assembly graph OLC Constructing a de Bruijn graph from reads Graph theory and assembly Genome assembly from de Bruijn graphs deBruijn - Euler deBruijn assembly software and publications deBruijn graph: a directed graph representing overlaps between sequences of symbols Credit: Wikipedia Konstantinos Krampis Genome Assembly Algorithms and Software
- 23. Introduction An alternative assembly graph OLC Constructing a de Bruijn graph from reads Graph theory and assembly Genome assembly from de Bruijn graphs deBruijn - Euler deBruijn assembly software and publications Konstantinos Krampis Genome Assembly Algorithms and Software
- 24. Introduction An alternative assembly graph OLC Constructing a de Bruijn graph from reads Graph theory and assembly Genome assembly from de Bruijn graphs deBruijn - Euler deBruijn assembly software and publications Konstantinos Krampis Genome Assembly Algorithms and Software
- 25. Introduction An alternative assembly graph OLC Constructing a de Bruijn graph from reads Graph theory and assembly Genome assembly from de Bruijn graphs deBruijn - Euler deBruijn assembly software and publications Konstantinos Krampis Genome Assembly Algorithms and Software
- 26. Introduction An alternative assembly graph OLC Constructing a de Bruijn graph from reads Graph theory and assembly Genome assembly from de Bruijn graphs deBruijn - Euler deBruijn assembly software and publications In a real genome scenario... Credit: Flicek and Birney 2009, Nature Methods 6, S6 - S12 Konstantinos Krampis Genome Assembly Algorithms and Software
- 27. Introduction An alternative assembly graph OLC Constructing a de Bruijn graph from reads Graph theory and assembly Genome assembly from de Bruijn graphs deBruijn - Euler deBruijn assembly software and publications Euler’s algorithm Using Euler’s algorithm we can find a path that visits each edge of the de Bruijn genome assembly graph once, in order to concatenate the edge labels and ”spell out” the assembly. Polynomial time! Credit: Wikipedia Konstantinos Krampis Genome Assembly Algorithms and Software
- 28. Introduction An alternative assembly graph OLC Constructing a de Bruijn graph from reads Graph theory and assembly Genome assembly from de Bruijn graphs deBruijn - Euler deBruijn assembly software and publications Euler assembler (the very first), Pevzner et al 2001 PNAS 98:9748-9753 Velvet assembler (more user friendly), Both those assemlers store the complete graph on the computer memory 512GB-1024GB for human genomes At JCVI we have two 1024GB (1TB) RAM servers for assembly others: ABYSS, YAGA, Contrail-Bio, PASHA parallel (distributed memory) assemblers on computer clusters Konstantinos Krampis Genome Assembly Algorithms and Software
- 29. Introduction An alternative assembly graph OLC Constructing a de Bruijn graph from reads Graph theory and assembly Genome assembly from de Bruijn graphs deBruijn - Euler deBruijn assembly software and publications Thank you! contact: kkrampis@jcvi.org We hire interns at the J. Craig Venter Institute: http://www.jcvi.org/cms/education/internship-program/ Some of my other projects - Cloud Computing: http://tinyurl.com/cloudbiolinux-jcvi http://www.cloudbiolinux.org Konstantinos Krampis Genome Assembly Algorithms and Software