1. A Hybrid Assembly System in Zebrafish Pooled Clones
Zemin Ning
The Wellcome Trust Sanger Institute 1

2. extended long reads of 1-2Kb
30-75 bp
Insert
~300 bp
Solexa assembly
Genome/Chromosome Assembly
Fishing WGS Reads
WGS Reads 5X
Combined Reads
FuzzyPath
Phusion or Phrap
Phusion
Solexa Reads

3. Read Coverage or Kmer Coverage

4. Minimum Kmer Coverage is 2

5. Kmer Extension & Repeat Junctions
Pileup of other reads like 454, Sanger etc
at a repeat junction
Consensus
Means to handle repeats:
- Base quality
- Read pair
- Fuzzy kmers
- Closely related reference
- 454 or Sanger reads

6. Pooled Clones: Zfish 9, Pig 3
Clone Name
Length (bp)
Finished
Cloning Vector
Species
Capillary Data Pathway
zH117H1
129221
Yes
pTARBAC2.1
D. rerio
/nfs/repository/d0012/zH117H1
zH141B18
119622
/nfs/repository/d0012/zH141B18
zH151M17
122622
/nfs/repository/d0014/zH151M17
zH117E7
139449
/nfs/repository/d0015/zH117E7
zH137D22
122615
/nfs/repository/d0023/zH137D22
zH97A24  
113538
/nfs/repository/d0027/zH97A24 
zH146D21
109862
/nfs/repository/d0040/zH146D21
zH140N19
118794
/nfs/repository/d0013/zH140N19
zH147D24
111470
/nfs/repository/d0011/zH147D24
bE2F11
170585
pTARBAC1.3_BamHI
S. scrofa
/nfs/repository/d0027/bE2F11
bE156J20
210831
/nfs/repository/d0041/bE156J20
bE240L11
216560* No
/nfs/repository/d0012/bE240L11
* Finished length may be shorter or longer once complete

7. Boundary of Solexa Contigs WGS DH reads and contigs

8. Mapping of Solexa Reads On the Reference

9. Zfish and “Pig” Clone Assemblies
Solexa reads:
Number of reads: million; Estimated size of covered region: Mbp;
Read length: 2x36bp;
Estimated read coverage: ~180X;
Insert size: / bp;
Zfish DH reads: 12,539
Assembly features: - contig stats Solexa Hybrid_Ctg Hybrid_Super
N contigs:
Bases: Mbp 1.68 Mbp 1.69 Mbp
N50 size: , ,817 74,598
Largest 23, , ,808
Averaged: , ,072 17,815
Coverage: ~72.6 % ~73% ~73%
Errors: ? ? ?

10. Second Set with 50 Zfish Clones
Solexa reads:
Number of reads: million; Estimated size of covered region : ~9.0 Mbp;
Read length: 2x54bp;
Estimated read coverage: ~190X;
Insert size: / bp;
Zfish DH capillary reads: 112,583
Assembly features: - contig stats Solexa Hybrid_Ctg Hybrid_Super
N contigs: 3,
Bases: Mbp 8.39 Mbp 8.43 Mbp
N50 size: , ,448 70,703
Largest 23, , ,224
Averaged: , ,194 23,493
Coverage: ~50% ~93% ~94%
Errors: ? ? ?

13. maq
ssaha2

14. maq
ssaha2

15. Contig of hybrid assembly
Contig of Zv8
Contig of hybrid assembly

16. Acknowledgements: Yong Gu James Bonfiled Hannes Ponstingl
Helen Beasley
Siobhan Whitehead
Michael Quail
Tony Cox