GigAssembler. Genome Assembly: A big picture

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Presentation transcript:

GigAssembler

Genome Assembly: A big picture

GigAssembler – Preprocessing 1. Decontaminating & Repeat Masking. 2. Aligning of mRNAs, ESTs, BAC ends & paired reads against initial sequence contigs. psLayout → BLAT 3. Creating an input directory (folder) structure.

The image from Reference: Jones NC, Pevzner PA, Introduction to Bioinformatics Algorithms, MIT press

RepBase + RepeatMasker

GigAssembler: Build merged sequence contigs (“rafts”)

Sequencing quality (Phred Score)

Base-calling Error Probability

GigAssembler: Build merged sequence contigs (“rafts”)

GigAssembler: Build sequenced clone contigs (“barges”)

GigAssembler: Build a “raft-ordering” graph

Add information from mRNAs, ESTs, paired plasmid reads, BAC end pairs: building a “bridge” Different weight to different data type: (mRNA ~ highest) Conflicts with the graph as constructed so far are rejected. Build a sequence path through each raft. Fill the gap with N. 100: between rafts 50,000: between bridged barges

Bellman-Ford algorithm

A B C DE Find the shortest path to all nodes Take every edge and try to relax it (N – 1 times where N is the count of nodes)

A B C DE Find the shortest path to all nodes Take every edge and try to relax it (N – 1 times where N is the count of nodes)

A B C DE Find the shortest path to all nodes START Inf. Take every edge and try to relax it (N – 1 times where N is the count of nodes)

A B C DE Find the shortest path to all nodes START Inf. +7 ( → A) +6 ( → A) Take every edge and try to relax it (N – 1 times where N is the count of nodes)

A B C DE Find the shortest path to all nodes START +7 ( → A) +6 ( → A) +2 ( → B) +4 ( → D) Take every edge and try to relax it (N – 1 times where N is the count of nodes)

A B C DE Find the shortest path to all nodes START +7 ( → A) +2 ( → B) +4 ( → D) +2 ( → C) Take every edge and try to relax it (N – 1 times where N is the count of nodes)

A B C DE Find the shortest path to all nodes START +7 ( → A) +4 ( → D) +2 ( → C) -2 ( → B) Take every edge and try to relax it (N – 1 times where N is the count of nodes)

A B C DE START +7 ( → A) +4 ( → D) +2 ( → C) -2 ( → B) Answer: A-D-C-B-E

Next-generation sequencing

Mardis ER, Annu. Rev. Genomics Hum. Genet., 2008 Illumina

Mardis ER, Annu. Rev. Genomics Hum. Genet., 2008 Illumina

Mardis ER, Annu. Rev. Genomics Hum. Genet., 2008 Roche/454

Mardis ER, Annu. Rev. Genomics Hum. Genet., 2008 SOLiD

An example of single molecule DNA sequencing, from Helicos (approx. 1 billion reads / run) Pushkarev, D., N.F. Neff, and S.R. Quake. Nat Biotechnol (2009) 27, Harris, T.D., et al. Science (2008) 320, 106-9

Mapping program Trapnell C, Salzberg SL, Nat. Biotech., 2009

Two strategies in mapping Trapnell C, Salzberg SL, Nat. Biotech., 2009