0
Finding the
viral biodiversity
in a biological
sample

nacho caballero
pasteur cayenne
Viral genome
Viral genome

Biological Sample
Isolate the
viruses
Viral genome
Viral genome

Biological Sample
Viral genome

Sequenced reads
Read-based alignment requires a
reference sequence
Read-based alignment requires a
reference sequence
De novo alignment depends
strongly on fragment size
De novo alignment depends
strongly on fragment size

Small K
De novo alignment depends
strongly on fragment size

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

Large K
Each sequencing error adds
k erroneous k-mers
Each sequencing error adds
k erroneous k-mers
Each sequencing error adds
k erroneous k-mers
There is an optimum fragment size
between 31 and 41 bp
16M
Total
Contig
Size
(bp)

normalized
not normalized

8M

0

k
Normalizing doesn’t
decrease performance

Number
of viruses

normalized
not normalized

k
Vipr reports more
viruses than NCBI

vipr protein
ncbi nucleotide
ncbi protein

Number
of viruses

k
Most assemblies contain
unique viruses

Number
of viruses

Assembly
Most assemblies contain
unique viruses

Number
of viruses

Assembly
Most assemblies contain
unique viruses

Number
of viruses

Assembly
Most contigs don’t align
to known viral sequences
Flavi, Pox,
Arteri and Corona
are the major
viral families
Understand differences
between assemblies
Understand differences
between assemblies
Measure viral
gene expression
Understand differences
between assemblies
Measure viral
gene expression
Determine the effects
of human perturbation
Finding the viral diversity in a biological sample
Finding the viral diversity in a biological sample
Finding the viral diversity in a biological sample
Finding the viral diversity in a biological sample
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Finding the viral diversity in a biological sample

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Transcript of "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
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