finding the viral diversity in a biological sample
DESCRIPTION
Lab meeting presentation.TRANSCRIPT
nacho caballero pasteur cayenne
Finding theviral biodiversityin a biological sample
Viral genome
Biological Sample
Viral genome
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
Total Contig
Size (bp)
16M
8M
0k
normalizednot normalized
There is an optimum fragment size between 31 and 41 bp
Normalizing doesn’t decrease performance
normalizednot normalized
Number of viruses
k
Vipr reports more viruses than NCBI
k
Number of viruses
vipr proteinncbi nucleotide
ncbi protein
Number of viruses
Assembly
Most assemblies contain unique viruses
Number of viruses
Assembly
Most assemblies contain unique viruses
Number of viruses
Assembly
Most assemblies contain unique viruses
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
Determine the effects of human perturbation
Understand differences between assemblies
Measure viral gene expression