Lab meeting presentation.

1. Finding the
viral biodiversity
in a biological
sample
nacho caballero
pasteur cayenne

2. Viral genome

3. Viral genome
Biological Sample

6. Isolate the
viruses

7. Viral genome

8. Viral genome
Biological Sample

9. Viral genome
Sequenced reads

10. Read-based alignment requires a
reference sequence

11. Read-based alignment requires a
reference sequence

12. De novo alignment depends
strongly on fragment size

13. De novo alignment depends
strongly on fragment size
Small K

14. De novo alignment depends
strongly on fragment size
Small K

15. De novo alignment depends
strongly on fragment size

16. De novo alignment depends
strongly on fragment size
Large K

19. Each sequencing error adds
k erroneous k-mers

20. Each sequencing error adds
k erroneous k-mers

21. Each sequencing error adds
k erroneous k-mers

22. There is an optimum fragment size
between 31 and 41 bp
16M
Total
Contig
Size
(bp)
normalized
not normalized
8M
0
k

23. Normalizing doesn’t
decrease performance
Number
of viruses
normalized
not normalized
k

24. Vipr reports more
viruses than NCBI
vipr protein
ncbi nucleotide
ncbi protein
Number
of viruses
k

25. Most assemblies contain
unique viruses
Number
of viruses
Assembly

26. Most assemblies contain
unique viruses
Number
of viruses
Assembly

27. Most assemblies contain
unique viruses
Number
of viruses
Assembly

28. Most contigs don’t align
to known viral sequences

29. Flavi, Pox,
Arteri and Corona
are the major
viral families

30. Understand differences
between assemblies

31. Understand differences
between assemblies
Measure viral
gene expression

32. Understand differences
between assemblies
Measure viral
gene expression
Determine the effects
of human perturbation