1. FuzzyPath Assemblies - from Mixed Solexa/454 Datasets to Extremely GC Biased Genomes Zemin Ning The Wellcome Trust Sanger Institute

2. Assembly Strategy Selexa reads assembler to extend long reads of 1-2Kb Genome/Chromosome Capillary reads assembler Phrap/Phusion forward-reverse paired reads 30-70 bp known dist ~500 bp 30-70 bp

3. Kmer Extension & Repeat Junctions

4. Handling of Single Base Variations

5. ACGTAACTAACAGTT 00 01 10 11 00 00 01 11 00 00 01 00 10 11 11 ACGTAACTCACAGTT 00 01 10 11 00 00 01 11 01 00 01 00 10 11 11 ACGTAACT ACAGTT 00 00 00 00 00 00 00 00 01 00 00 00 00 00 00 Fuzzy Kmers Number of Mismatches between Two Kmers

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

7. Pileup of Solexa and 454 Reads

8. Solexa reads : Number of reads: 3,084,185; Finished genome size: 2,007,491 bp; Read length:39 and 36 bp; Estimated read coverage: ~55X; Number of 454 reads:100,000; Read coverage of 454:10X; Assembly features: - contig stats Total number of contigs: 73; Total bases of contigs: 1,999,817 bp N50 contig size: 62,508; Largest contig:162,190 Averaged contig size: 27,394; Contig coverage over the genome: ~99 %; Contig extension errors: 2 Mis-assembly errors:3 S.Suis P1/7 Solexa/454 Assembly

9. Solexa reads : Number of reads: 6,000,000; Finished genome size: ~4.8 Mbp; Read length:2x37 bp; Estimated read coverage: ~92.5 X; Insert size: 170/50-300 bp; Assembly features: - contig stats Solexa454 Total number of contigs: 75;390 Total bases of contigs: 4.80 Mbp4.77 Mb N50 contig size: 139,35325,702 Largest contig:395,600 62,040 Averaged contig size: 63,96912,224 Contig coverage on genome: ~99.8 %99.4% Contig extension errors: 0 Mis-assembly errors:04 Salmonella seftenberg Solexa Assembly from Pair-End Reads

10. Solexa reads : Number of reads: 7,055,348; Finished genome size: 5.35 Mbp; Read length:2x36bp; Estimated read coverage: ~95X; Insert size: 170/50-300 bp; Assembly features: - contig stats Total number of contigs: 168; Total bases of contigs: 5.19 Mbp N50 contig size: 85,886; Largest contig:337,768 Averaged contig size: 30,886; Contig coverage over the genome: ~99 %; Contig extension errors: 1 Mis-assembly errors:2 E.Coli strain 042 Assembly

11. Solexa reads : Number of reads: 6,346,317; Finished genome size: 4.7 Mbp; Read length:33 bp; Estimated read coverage: ~40 X; Shredded reference of SpA: 10X; Assembly features: - contig stats Total number of contigs: 66; Total bases of contigs: 4,615,704 bp N50 contig size: 168,793; Largest contig:401,700 Averaged contig size: 69,934; Contig coverage over the genome: ~98 %; Contig extension errors: 0 Mis-assembly errors:2 Salmonella delhi5 Solexa Assembly Guided by A Close Reference

12. The Malaria Genome Project

13. library organismread lengthMb sequencegenomemean generatedsize (Mb)coverage PCR-free B. pertussis ST242 x 769074.1221 PCR-free E. coli 0422 x 765735.3108 PCR-free P. falciparum 3D72 x 76148623.065 PCR-free B. pertussis ST242 x 364524.1110 PCR-free P. falciparum 3D72 x 36100823.044 PCR-free E. coli 0422 x 369585.3181 standard-245 P. falciparum 3D72 x 35219823.096 standard-368 P. falciparum 3D72 x 35262823.0115 standard-851 P. falciparum 3D72 x 3547423.021 standard-883 P. falciparum clin2 x 36399423.0175 Datasets with Various GC Content GC 68.0% 50.5% 19.0% 50.8% 19.0% 68.0% 19.0%

18. Solexa reads :2x36 bp2x76 bp Number of reads: 14.0m9.77m Finished genome size: 23 Mbp23 Mbp Estimated read coverage: 43x64x Insert size: 170 bp170 bp Assembly features: Total number of contigs: 26,92622839 Total bases of contigs: 19.2 Mbp21.1 Mb N50 contig size: 14561621 Largest contig:9106 9825 Averaged contig size: 706923 Contig coverage on genome: ~83.5 %91.7% Contig extension errors: ?? Mis-assembly errors:?? Malaria 3D7 Assemblies

19. Acknowledgements:  Yong Gu  Ben Blackburne  Hannes Ponstingl  Daniel Turner  Michael Quail  Tony Cox  Richard Durbin