Aug2015 analysis team 08 genome in a bottle alex hastie 2015_final

1. GIAB August 2015
Irys: Genome Maps for
Sequence Assembly and
Structural Variation

2. 2
Genome Mapping in Platinum Genome Assembly
De novo assembly
Scaffolding
SV calling and
validation
Orthogonal validation and
Chimera detection

3. 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. 4
De Novo Assembly of Chr1 q-arm Pericentromeric Region
PacBio
Hg19 Chr1 144M-154M
BNG
Hg19 Chr1 144M-154M

5. 5
Genome Map Provides Orthogonal Cross Validation of
Sequence Assemblies and Conflict Flagging
No Discrepancies
PacBio
BNG
PacBio
BNG
BNG
No Discrepancies

6. 6
Conflict Resolution Example
Ben Rosen, Derek Bickhart et al., USDA

7. 7
Orthogonal Validation of Structural Variation Calls
PacBio
Hg19-Chr1
7 kb Insertion at
9.675 Mb – 9.688 Mb
BNG
Hg19-Chr1

8. 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. 9
Acknowledgments
• GIAB
• BioNano Genomics
− Han Cao
− Zeljko Dzakula
− Ernest Lam
− Andy Pang
− Thomas Anantharaman
− Khoa Pham
− Will Stedman
• Mt. Sinai
− Ali Bashir