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A cost-effective approach to diploid genome assembly using
sequence graphs
Shilpa Garg
Postdoc
Church lab
Harvard Medical School
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Diploid genome assembly
A C G T C T
C C G T A T C G T
A C G T A T
T A C G T A T
C C G T A T G T
Input: Reads
Diploid assemblies
Applications:
● Personalized medicine
● Human migration, evolutionary selection and population structure
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Different approaches
Reference-based haplotyping
Reference genome
Aligned reads
Haplotypes
Drawbacks
● Reference bias
● Does not work for structural variants (SVs)
Tools: WhatsHap, HapCut, HapCol
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De novo assembly
Different approaches
Reference-based haplotyping
Reference genome
Aligned reads
Haplotypes
Drawbacks
● Reference bias
● Does not work for structural variants (SVs)
r1
r2
r3
r4
r5
r1 r2 r3
r4r5
Assembly
graph
Reads
Tools: WhatsHap, HapCut, HapCol
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De novo assembly
Different approaches
Reference-based haplotyping
Reference genome
Aligned reads
Haplotypes
Drawbacks
● Reference bias
● Does not work for structural variants (SVs)
r1
r2
r3
r4
r5
r1 r2 r3
r4r5
Assembly
graph
assembly
Reads
Tools: WhatsHap, HapCut, HapCol
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7.
De novo assembly
Different approaches
Reference-based haplotyping
Reference genome
Aligned reads
Haplotypes
Drawbacks
● Reference bias
● Does not work for structural variants (SVs)
Drawbacks
● Assumption: haploid assembly
● Require high coverage data
r1
r2
r3
r4
r5
r1 r2 r3
r4r5
Assembly
graph
assembly
Reads
Tools: WhatsHap, HapCut, HapCol
Tools:
Genome assembly: Canu, SPAdes…
Diploid genome assembly: Falcon Unzip,
TrioCanu
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Why graph-based approach?
SNV SV SV SNV
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Phasing bubble chains
SNV SV SV SNV
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Phasing bubble chains
SNV SV SV SNV
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Our diploid assembly pipeline
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Single individual

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Our diploid assembly pipeline
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Single individual Trios

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Advantages
- Generalized to be applied to genomes of any complexity
- Different het rate and repeat content
- Phase complex SVs
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Results
We require as low as 15x coverage of long
reads from each individual
in a trio
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Conclusion
- Apply pipeline on GIAB trio samples from PGP
- Fill gaps in PGP-1 genome and other variety of samples
- Apply haplotype-aware assembly to diverse human genomes, including
clinically relevant regions, to understand complex biology
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- Developed pipeline for diploid assembly for single individuals and trios
- Demonstrated on genomes with various het rate
Next steps:
Open for collaborations and recruiting people at Church lab

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Acknowledgements
George Church
Tobias Marschall
Richard Durbin
...
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Thanks