Finding the viral diversity in a biological sample
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Finding the viral diversity in a biological sample

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    Finding the viral diversity in a biological sample Finding the viral diversity in a biological sample Presentation Transcript

    • 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