SNP Workshop III
NGS and SNP Discovery
NGS and SNP Discovery




                        !
Challenges
Sharing
NGS and SNP Discovery
NGS and SNP Discovery
NGS and SNP Discovery




                        !"""#$%&#'%())&*+,*+#-(.$#/$(0/#,*#$%&#%,+%#$%.12+%-2$#
                ...
NGS and SNP Discovery




                        credit: NOAA
SNP Discovery in Pacific herring using 454
transcriptome sequencing

Steven Roberts, Jim Seeb, Lisa Seeb, Lorenz Hauser,
Un...
Credit: EXXON VALDEZ Oil Spill Trustee Council
Prince
Togiak     William Sound
         Kodiak
                           Sitka
Approach

           • Pooled Individuals to
           generate 2 libraries
            • Liver
            • Testes

   ...
Sequencing Output (combined)




                         Reads: 1.9 million
                         Average Length: 272 ...
Comparing Tissues




                    10622 features
                    not expressed
                       in Liver...
Annotation (combined)




!
SNP Discovery


         16,000 SNPs

               per library - ~9300 SNPs


                                 Annotatio...
transversions                         transitions
                                              !")$%,-(%



    SNP Disco...
transversions                           transitions
                                                !")$%,-(%



    SNP D...
Targeting SNPs


                 xenobiotic response
Synonymous and NonSynonymous              workflow


consensus       EMBOSS
sequences        getorf



  SNP           refe...
Synonymous and NonSynonymous    workflow




                      2514 NonSynonymous
NonSynonymous
NonSynonymous




                stress response
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Herring SNP Sneak Peak

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Sneak peak at SNP III presentation

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Herring SNP Sneak Peak

  1. 1. SNP Workshop III
  2. 2. NGS and SNP Discovery
  3. 3. NGS and SNP Discovery !
  4. 4. Challenges
  5. 5. Sharing
  6. 6. NGS and SNP Discovery
  7. 7. NGS and SNP Discovery
  8. 8. NGS and SNP Discovery !"""#$%&#'%())&*+,*+#-(.$#/$(0/#,*#$%&#%,+%#$%.12+%-2$# +&*1$0-,*+#"""#,*#3&.0#-1)041.-%,'#/-&',&/5
  9. 9. NGS and SNP Discovery credit: NOAA
  10. 10. SNP Discovery in Pacific herring using 454 transcriptome sequencing Steven Roberts, Jim Seeb, Lisa Seeb, Lorenz Hauser, University of Washington School of Aquatic and Fishery Sciences William Templin Alaska Division of Fish and Game Division of Commercial Fisheries Exxon Valdez Oil Spill Trustee Council
  11. 11. Credit: EXXON VALDEZ Oil Spill Trustee Council
  12. 12. Prince Togiak William Sound Kodiak Sitka
  13. 13. Approach • Pooled Individuals to generate 2 libraries • Liver • Testes • De novo Assembly • Annotation • SNP Discovery
  14. 14. Sequencing Output (combined) Reads: 1.9 million Average Length: 272 bp Matched: 1.7 million Contigs: 47,267 Average Length of Contigs: 728 bp
  15. 15. Comparing Tissues 10622 features not expressed in Liver 14190 features not expressed in Testes
  16. 16. Annotation (combined) !
  17. 17. SNP Discovery 16,000 SNPs per library - ~9300 SNPs Annotation of = corresponding features ! ! all features
  18. 18. transversions transitions !")$%,-(% SNP Discovery *"#$%,-(% !"#$%&'(% !"*$%,&(% )"#$%,,(% )"*$%&+(% !
  19. 19. transversions transitions !")$%,-(% SNP Discovery *"#$%,-(% !"#$%&'(% !"*$%,&(% )"#$%,,(% )"*$%&+(% ! tinyurl.com/herringSNP
  20. 20. Targeting SNPs xenobiotic response
  21. 21. Synonymous and NonSynonymous workflow consensus EMBOSS sequences getorf SNP reference Detection assembly 2514 NonSynonymous Annotate Filter based SNP Positive on e-value Features 7017 SNPs
  22. 22. Synonymous and NonSynonymous workflow 2514 NonSynonymous
  23. 23. NonSynonymous
  24. 24. NonSynonymous stress response

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