GIAB August 2015

Irys: Genome Maps for Sequence Assembly and

Structural Variation

2

Genome Mapping in Platinum Genome Assembly

De novo assembly

Scaffolding

SV calling and validation

Orthogonal validation and Chimera detection

3

Sample molecule, assembly, and variation summary

Molecule GM24143 Mother

GM24149 Father

GM24385 Son

Molecules >150 kb # 1106746 933742 1320289

Molecule N50 (kb) 257.4 306.2 264.6

Molecule coverage (x) 91.8 87.3 111.6

Assembly GM24143 Mother

GM24149 Father

GM24385 Son

Assembly map (#) 1092 1094 1098

Total map len (Mb) 2855.1 2884.9 2876.8

Map N50 (Mb) 4.44 4.48 4.59

Total map len / Ref len 0.91 0.92 0.91

Total NR map len / Ref len 0.90 0.91 0.90

Variation* GM24143 Mother

GM24149 Father

GM24385 Son

Insertion 570 669 626

Deletion 320 284 333

Inversion breakpoint 20 26 29

4

De Novo Assembly of Chr1 q-arm Pericentromeric Region

PacBio

Hg19 Chr1 144M-154M

BNG

Hg19 Chr1 144M-154M

5

Genome Map Provides Orthogonal Cross Validation of Sequence Assemblies and Conflict Flagging

No Discrepancies

PacBio

BNG

PacBio

BNG

BNG

No Discrepancies

6

Conflict Resolution Example

Ben Rosen, Derek Bickhart et al., USDA

7

Orthogonal Validation of Structural Variation Calls

PacBio

Hg19-Chr1

7 kb Insertion at9.675 Mb – 9.688 Mb

BNG

Hg19-Chr1

8

Summary

• Fully de novo genome map assembly for genome structure

• Validation of sequence assembly by orthogonal verification

• Hybrid scaffolding of sequence assemblies• Structural variation detection• Structural variation validation by genome map and

single molecule alignment

9

Acknowledgments

• GIAB• BioNano Genomics−Han Cao−Zeljko Dzakula−Ernest Lam−Andy Pang−Thomas Anantharaman−Khoa Pham−Will Stedman

• Mt. Sinai−Ali Bashir