finding the viral diversity in a biological sample

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