GigAssembler

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GigAssembler
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Genome Assembly A big picture
http//www.nature.com/scitable/content/anatomy-of-
whole-genome-assembly-20429
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GigAssembler Preprocessing

• Decontaminating Repeat Masking.
• Aligning of mRNAs, ESTs, BAC ends paired reads
  against initial sequence contigs.
• psLayout ? BLAT
• Creating an input directory (folder) structure.

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http//www.triazzle.com The image from
http//www.dangilbert.com/port_fun.html Reference
Jones NC, Pevzner PA, Introduction to
Bioinformatics Algorithms, MIT press
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RepBase RepeatMasker
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GigAssembler Build merged sequence contigs
(rafts)
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Sequencing quality (Phred Score)
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Sequencing quality (Phred Score)
Base-calling Error Probability
http//en.wikipedia.org/wiki/Phred_quality_score
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GigAssembler Build merged sequence contigs
(rafts)
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GigAssembler Build merged sequence contigs
(rafts)
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GigAssembler Build sequenced clone contigs
(barges)
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GigAssembler Build a raft-ordering graph
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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

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Bellman-Ford algorithm
http//compprog.wordpress.com/2007/11/29/one-sourc
e-shortest-path-the-bellman-ford-algorithm/
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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)
5
B
C
-2
6
8
A
-3
7
-4
7
D
E
2
9
16
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)
5
B
C
-2
6
8
A
-3
7
-4
7
D
E
2
9
17
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)
5
B
C
Inf.
Inf.
-2
6
8
A
-3
7
START
-4
7
D
E
2
Inf.
Inf.
9
18
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)
5
B
C
6 (? A)
Inf.
-2
6
8
A
-3
0 START
7
-4
7
D
E
2
7 (? A)
Inf.
9
19
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)
5
B
C
6 (? A)
4 (? D)
-2
6
8
A
-3
0 START
7
-4
7
D
E
2
7 (? A)
2 (? B)
9
20
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)
5
B
C
4 (? D)
2 (? C)
-2
6
8
A
-3
0 START
7
-4
7
D
E
2
7 (? A)
2 (? B)
9
21
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)
5
B
C
4 (? D)
2 (? C)
-2
6
8
A
-3
0 START
7
-4
7
D
E
2
7 (? A)
-2 (? B)
9
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Answer A-D-C-B-E
5
B
C
4 (? D)
2 (? C)
-2
6
8
A
-3
0 START
7
-4
7
D
E
2
7 (? A)
-2 (? B)
9
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Next-generation sequencing
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Mardis ER, Annu. Rev. Genomics Hum. Genet., 2008
Illumina
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Mardis ER, Annu. Rev. Genomics Hum. Genet., 2008
Illumina
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Mardis ER, Annu. Rev. Genomics Hum. Genet., 2008
Roche/454
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Mardis ER, Annu. Rev. Genomics Hum. Genet., 2008
SOLiD
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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, 847-50 Harris, T.D., et al.
Science (2008) 320, 106-9
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Mapping program
Trapnell C, Salzberg SL, Nat. Biotech., 2009
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Two strategies in mapping
Trapnell C, Salzberg SL, Nat. Biotech., 2009