1. Cross_genome: Assembly Scaffolding using Cross-species Synteny
Zemin Ning
High Performance Assembly 1

2. Can synteny help? And How?
Scaffolding
Contig gap closure

3. RACA - Reference-assisted chromosome assembly

4. Q = scaff(i)*232 + contig_loci(j) Lattice of Target - Reference
Target sequence
Reference
Scaffold 1
Scaffold 2
Scaffold 3
Q = scaff(i)*232 + contig_loci(j)
Lattice of Target -
Reference

5. After Noise Cleaning Gap_size = Y - X Scaffold 3 Scaffold 2 Scaffold 1
Target sequence
Reference
Scaffold 1
After Noise Cleaning
Gap_size = Y - X Y
Scaffold 3 X
Scaffold 2

6. Cases Shouldn’t Join Reference Target Reference Target Gap_size
Scaffold 1
Scaffold 2
Reference
Target
Gap_size
Scaffold 1
Scaffold 2

7. GAGE: Human Chr14 and RACA using Orangutan
Assembler
N_bases
N_scaffs
N50 (Mb)
Original
88.8
418
81.6
Allpahts-LG
RACA
86.8
Cross_genome 89
221
85.5
78.6
1472
0.37
Bambus2
72.1
1094
13.7
86.5
498
0.4
CABOG
81.4
86.3 46
89.7
0.88
MSR-CA
83.4
89.6
94.7
30975
0.075
SGA
57.4
94.8
29662
77.3
108
38477
0.453
SOAPdenovo
84.4
102.8
12955
78.9
143.8
61455
0.84
Velvet
123
139.4
3278
8.71

8. Scaffold N50 for Other Genome Assemblies
Original Cross_g References Panda Mb 25Mb Dog, Human
Tibetan Antelope 2.6Mb 42Mb Cattle, Dog, Human
Tasmanian Devil 1.8Mb 6.8Mb Opossum
Availability
ftp://ftp.sanger.ac.uk/pub/users/zn1/merge/cross_genome/

9. Improve gorilla assembly using human reference
Contig gap size re-estimation
Improve gorilla assembly using human reference
Combined Gorilla-Human Assembly
Read Alignment
Pair-wise/Multiple
Read Clustering
Local Assembly
Final Gorilla Assembly

10. Re-estimate Contig Gap Sizes from Reference
New gap size
Local assembly based on clustered reads
Ref seq inserted
Gap size
New gap size
Target sequence
Reference sequence

11. Assemblies using Synteny-guided Method Gorilla Genome - Real Data
Human Chr6 - Simulation
Gorilla Genome - Real Data
Reads: 2x100 with 500bp insert
60X
Original
Assembly
Contig N50
24.3kb
13.5kb
Average contig length
6850bp
6940bp
N of clusters ( pairs)
504
5807
43.7kb
24.0kb
Gap closed
7809
10433
N of base errors in gap
closed regions
256 subs and
12 indels (24bps)
N/A

12. Gorilla - Merge with other De novo Assemblies Original assembly (dev5)
Merge with Fermi*
Merge with Masurca+
Contig N50
13.5kb
30.2kb
53.1kb
Average length
6850
12577
18768
Largest contig
215kb
391.2kb
448.8kb
N of gaps closed
182661
257167
*Fermi assembler:
+Masurca assembler:

13. Gs = (Kn – Ks)/D = 4.5x109
Kn = 125.4x109 – Total number of kmer words;
Ks = 2.4x109 - Number of single copy kmer words;
D = Depth of kmer occurrence

14. Original Contig (query) against New Assembly after Contig Break

15. Alignment Inconsistency

16. Original Contig (query) against New Assembly after Contig Break

17. Alignment Inconsistency

18. The Gorilla Assemblies
Original New
Total number of contigs: , ,139
N50 contig size: kb 23.9kb
Largest contig: 191, ,733
Averaged contig size:

19. Acknowledgements: Hanness Ponstingl
Frank Liu – Nanjing University of Information Technology (NUIT)
Yan Li – (NUIT)
Gorilla genome sequencing data
BGI – Panda and Tibetan Antelope assemblies