The Genome Assembly Problem
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Transcript of The Genome Assembly Problem
TheGenomeAssemblyProblem
alightningtalk
MarkChang
TheGenomeAssemblyProblem
ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT
ACCTCAGAACCCCGCAGTCACGTAGCGTTTGTGGGTACCTCGTGTCTAGT
FragmentedandSequenced
FindingOverlaps
Recunstruction
CGTAGCGTTTGTGGGTACCTCAGAACCCAACCCCGCAGTCACGTAG GTGGGTACCTCGTG
TCGTGTCTAGT
Genome
ACCTCAGAACCCAACCCCGCAGTCACGTAG
GTGGGTACCTCGTGCGTAGCGTTTGTGGGTTCGTGTCTAGT
Short-reads
FindingOverlaps
• Itisveryhardtofindtheoverlapsbetweenmillionsofshort-reads
ACCTCAGAACCC
AACCCCGCAGTCACGTAG
GTGGGTACCTCGTGCGTAGCGTTTGTGGGT
TCGTGTCTAGT
FindingOverlaps
• UsingdeBruijn Graphs
AABCDC
ABC
BCC
CCD
CDA
DCC
AABCCDCCDAgraphtraversal
AABCCDCCDAconverttodeBruijn Graph
UsingdeBruijn Graphs
• Converttheshort-reads intok-mers
ACCTCAGAACCC AACCCCGCAGTCACGTAG
GAACCAGAAC
CAGAA
ACCTCCCTCACTCAGTCAGA
AACCC
AACCC
ACGTACACGT
GCAGTCGCAGCCGCACCCGC
ACCCCCCCCG
CGTAG
UsingdeBruijn Graphs
• Builddebruijn graphfromk-mers
GAACCAGAACCAGAA
ACCTCCCTCACTCAGTCAGA
AACCC
GAACC AGAAC CAGAA
ACCTC CCTCA CTCAG TCAGA
AACCC
UsingdeBruijn Graphs
• Builddebruijn graphfromk-mers
GAACC AGAAC CAGAA
ACCTC CCTCA CTCAG TCAGA
AACCC
AACCC
ACGTACACGTGCAGTCGCAGCCGCACCCGC
ACCCCCCCCG
CGTAG
ACGTA CACGT GCAGT CGCAG
CCGCACCCGCACCCC CCCCG
CGTAG
UsingdeBruijn Graphs
• Graphtraversal
ACCTCAGAACCCCGCAGTCACGTAG
GAACC AGAAC CAGAA
ACCTC CCTCA CTCAG TCAGA
AACCC
ACGTA CACGT GCAGT CGCAG
CCGCACCCGCACCCC CCCCG
CGTAG
Reference
• TheGenomeAssemblyProblem• http://homolog.us/Tutorials/index.php?p=1.1&s=1
![Question: is de novo genome assembly a solved problem with ...rayan.chikhi.name/pdf/2019-july-19-cgsi.pdf · Genome assembly is NP-hard.[Medvedev, Brudno 2007] If all repeats are](https://static.fdocuments.in/doc/165x107/5ed8d1a96714ca7f47689fac/question-is-de-novo-genome-assembly-a-solved-problem-with-rayan-genome-assembly.jpg)
![Fast Virus and Bacteria Genome Sequencing by Compatible ... · The genome map assembly problem can be abstracted as an instance of the big-bag matching problem [10]. A bag is a multiset,](https://static.fdocuments.in/doc/165x107/5ed8d1c86714ca7f47689fe4/fast-virus-and-bacteria-genome-sequencing-by-compatible-the-genome-map-assembly.jpg)
