The Genome Assembly Problem

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Mark Chang

a lightning talk about the de Bruijn Graphs assembling algorithm

Technologie

The Genome Assembly
Problem
a lightning talk
Mark Chang

The Genome Assembly Problem
ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT
ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT
Fragmented and Sequenced
Finding Overlaps
Recunstruction
CGTAGCGTTTGTGGGTACCTCAGAACCC
AACCCCGCAGTCACGTAG GTGGGTACCTCGTG
TCGTGTCTAGT
Genome
ACCTCAGAACCC
AACCCCGCAGTCACGTAG
GTGGGTACCTCGTGCGTAGCGTTTGTGGGT
TCGTGTCTAGT
Short-reads

Finding Overlaps
• It is very hard to find the overlaps between millions of short-reads
ACCTCAGAACCC
AACCCCGCAGTCACGTAG
GTGGGTACCTCGTGCGTAGCGTTTGTGGGT
TCGTGTCTAGT

Finding Overlaps
• Using de Bruijn Graphs
AAB
CDC
ABC
BCC
CCD
CDA
DCC
AABCCDCCDA
graph traversal
AABCCDCCDA
convert to de Bruijn Graph

Using de Bruijn Graphs
• Convert the short-reads into k-mers
ACCTCAGAACCC AACCCCGCAGTCACGTAG
GAACC
AGAAC
CAGAA
ACCTC
CCTCA
CTCAG
TCAGA
AACCC
AACCC
ACGTA
CACGT
GCAGT
CGCAG
CCGCA
CCCGC
ACCCC
CCCCG
CGTAG

Using de Bruijn Graphs
• Build de bruijn graph from k-mers
GAACC
AGAAC
CAGAA
ACCTC
CCTCA
CTCAG
TCAGA
AACCC
GAACC AGAAC CAGAA
ACCTC CCTCA CTCAG TCAGA
AACCC

Using de Bruijn Graphs
• Build de bruijn graph from k-mers
GAACC AGAAC CAGAA
ACCTC CCTCA CTCAG TCAGA
AACCC
AACCC
ACGTA
CACGT
GCAGT
CGCAG
CCGCA
CCCGC
ACCCC
CCCCG
CGTAG
ACGTA CACGT GCAGT CGCAG
CCGCACCCGCACCCC CCCCG
CGTAG

Using de Bruijn Graphs
• Graph traversal
ACCTCAGAACCCCGCAGTCACGTAG
GAACC AGAAC CAGAA
ACCTC CCTCA CTCAG TCAGA
AACCC
ACGTA CACGT GCAGT CGCAG
CCGCACCCGCACCCC CCCCG
CGTAG

Reference
• The Genome Assembly Problem
• http://homolog.us/Tutorials/index.php?p=1.1&s=1

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The Genome Assembly Problem

1. The Genome Assembly Problem a lightning talk Mark Chang

2. The Genome Assembly Problem ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT Fragmented and Sequenced Finding Overlaps Recunstruction CGTAGCGTTTGTGGGTACCTCAGAACCC AACCCCGCAGTCACGTAG GTGGGTACCTCGTG TCGTGTCTAGT Genome ACCTCAGAACCC AACCCCGCAGTCACGTAG GTGGGTACCTCGTGCGTAGCGTTTGTGGGT TCGTGTCTAGT Short-reads

3. Finding Overlaps • It is very hard to find the overlaps between millions of short-reads ACCTCAGAACCC AACCCCGCAGTCACGTAG GTGGGTACCTCGTGCGTAGCGTTTGTGGGT TCGTGTCTAGT

4. Finding Overlaps • Using de Bruijn Graphs AAB CDC ABC BCC CCD CDA DCC AABCCDCCDA graph traversal AABCCDCCDA convert to de Bruijn Graph

5. Using de Bruijn Graphs • Convert the short-reads into k-mers ACCTCAGAACCC AACCCCGCAGTCACGTAG GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC AACCC ACGTA CACGT GCAGT CGCAG CCGCA CCCGC ACCCC CCCCG CGTAG

6. Using de Bruijn Graphs • Build de bruijn graph from k-mers GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC

7. Using de Bruijn Graphs • Build de bruijn graph from k-mers GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC AACCC ACGTA CACGT GCAGT CGCAG CCGCA CCCGC ACCCC CCCCG CGTAG ACGTA CACGT GCAGT CGCAG CCGCACCCGCACCCC CCCCG CGTAG

8. Using de Bruijn Graphs • Graph traversal ACCTCAGAACCCCGCAGTCACGTAG GAACC AGAAC CAGAA ACCTC CCTCA CTCAG TCAGA AACCC ACGTA CACGT GCAGT CGCAG CCGCACCCGCACCCC CCCCG CGTAG

9. Reference • The Genome Assembly Problem • http://homolog.us/Tutorials/index.php?p=1.1&s=1