combining de bruijn graph, overlap graph and microassembly for de novo genome assembly
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TRANSCRIPT
Combining de Bruijn graph, overlap graph and
microassembly for de novo genome assembly
A. Alexandrov, S. Kazakov, S. Melnikov, A. Sergushichev, P. Fedotov, F. Tsarev,
A. Shalyto
Genome Assembly Algorithms Laboratory
St. Petersburg National Research University of Information Technologies, Mechanics and Optics
Kazan, 23 Nov 2012
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Algorithm
Error correction
Quasi-contig
assembly
Initial contig
assembly
Contig micro-
assembly
De Bruijn graph
Overlap graph
Scaffolding
33
Error correction
• K-mers – substrings of length k.• “Trusted” and “untrusted” k-mers.• Replace “untrusted” k-mers with the
“trusted” ones.• If all the k-mers don’t fit into memory.
• Divide them into buckets.• Process the buckets independently.
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Quasicontig assembly
??? GTCCATGC
ATGCATGCAGTG GTCCATGC
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De Bruijn graph
De Bruijn graph for a set of strings S:
● V =
6
De Bruijn graph example (1)
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De Bruijn graph example (2)
AGT GTG
GTC TCA CAT ATC TCC
CCA
CAA
AACACA
CAC
CAGAGGGGAGAG
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Quasicontig assembly
• Build the de Bruijn graph.
• For each pair of reads (r1, r2) find the path between the first k-mer of r1 and the last k-mer of r2.
• The path has to be of appropriate length.
• The path has to be unique.
9
De Bruijn graph example (3)
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De Bruijn graph example (4)
Unique paths correspond to quasicontigs
1212
Initial contig assembly
• Overlap– Suffix array– Inexact overlaps
• Layout– Overlap graph
• Consensus
13
Contig microassembly
• There are paired reads that map to different contigs.
• There are pairs of reads, one of which maps to one of the contigs and the other one maps to the gap between the contigs.
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Contig microassembly algorithm
• Use Bowtie to find the positions of reads in contigs.
• Find all the pairs of contigs connected by many reads.
• Build the de Bruijn graph using the reads that map to at least one of the chosen contigs.
• Use the quasicontig assembly algorithm to fill the gap.
15
Results
• E. Coli genome – 4,5 million nucleotides.
• SRR001665 library, fragment size – 200, read length – 36, coverage – 160.
• Before microassembly – 525 contigs, N50 = 17804.
• After microassembly – 247 contigs, N50 = 53720.
• ABySS – 632 contigs, N50 = 64280.
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Web-service
• http://genome.ifmo.ru/cloud
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Acknowledgements
• K. Skryabin, E. Prokhorchuk from “Bioengineering” center, for introduction to bioinformatics.
• D. Alexeev, from NRI PCM, for the invitation to this conference.