Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Finding the viral diversity in a biological sample

537 views

Published on

Lab meeting presentation.

Published in: Education, Technology
  • Be the first to comment

  • Be the first to like this

Finding the viral diversity in a biological sample

  1. 1. Finding the viral biodiversity in a biological sample nacho caballero pasteur cayenne
  2. 2. Viral genome
  3. 3. Viral genome Biological Sample
  4. 4. Isolate the viruses
  5. 5. Viral genome
  6. 6. Viral genome Biological Sample
  7. 7. Viral genome Sequenced reads
  8. 8. Read-based alignment requires a reference sequence
  9. 9. Read-based alignment requires a reference sequence
  10. 10. De novo alignment depends strongly on fragment size
  11. 11. De novo alignment depends strongly on fragment size Small K
  12. 12. De novo alignment depends strongly on fragment size Small K
  13. 13. De novo alignment depends strongly on fragment size
  14. 14. De novo alignment depends strongly on fragment size Large K
  15. 15. Each sequencing error adds k erroneous k-mers
  16. 16. Each sequencing error adds k erroneous k-mers
  17. 17. Each sequencing error adds k erroneous k-mers
  18. 18. There is an optimum fragment size between 31 and 41 bp 16M Total Contig Size (bp) normalized not normalized 8M 0 k
  19. 19. Normalizing doesn’t decrease performance Number of viruses normalized not normalized k
  20. 20. Vipr reports more viruses than NCBI vipr protein ncbi nucleotide ncbi protein Number of viruses k
  21. 21. Most assemblies contain unique viruses Number of viruses Assembly
  22. 22. Most assemblies contain unique viruses Number of viruses Assembly
  23. 23. Most assemblies contain unique viruses Number of viruses Assembly
  24. 24. Most contigs don’t align to known viral sequences
  25. 25. Flavi, Pox, Arteri and Corona are the major viral families
  26. 26. Understand differences between assemblies
  27. 27. Understand differences between assemblies Measure viral gene expression
  28. 28. Understand differences between assemblies Measure viral gene expression Determine the effects of human perturbation

×