Combining PacBio with short read technology for improved de novo genome assembly
1. The best of both worlds
Combining PacBio with short read technology
for improved de novo genome assembly
Lex Nederbragt, NSC and CEES
lex.nederbragt@bio.uio.no
4. What is a genome assembly
Hierarchical structure
reads
contigs
scaffolds
5. Sequence data
Reads
reads
contigs
scaffolds
original DNA
fragments
original DNA
fragments
Sequenced ends
http://www.cbcb.umd.edu/research/assembly_primer.shtml
28. Solutions for assembly (3)
PacBioToCA
Error correct with short reads
Celera assembler
http://schatzlab.cshl.edu/presentations/2012-01-17.PAG.SMRTassembly.pdf
37. The goal
23 pseudochromosomes
Longer contigs
Below 5% gap bases
PacBio to the rescue?
38. The approach
SMRTBell'template'
Libraries
Standard'Sequencing'
Generates& pass& ea
one& on&
Large Insert& Sizes
Large& Sizes&
Insert sequenced&
Aim for looooong insert sizes
Circular'Consensus'Sequencing'
Small&
Insert&
Sizes&
Generates&
mul8ple&
passes
sequenced&
39. SMRTBell'template' The approach
Sequencing
Standard'Sequencing'
Generates& pass& each&
one& on& molecule&
Large Insert& Sizes
Large& Sizes&
Insert Single pass
sequenced&
Sequence with 90 minute movies
Circular'Consensus'Sequencing'
Small&
Insert&
Sizes&
Generates&
mul8ple&
passes& each&
on& molecule&
10 x coverage in reads of at least 3000 bp sequenced&
No, we don’t throw this away…