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Viral biodiversity in rodents
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Viral biodiversity in rodents

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I was invited to give a short presentation about the tools that I use for my research in Cayenne, French Guiana (sickle, velvet, digital normalization (khmer), krona, awk and others).

I was invited to give a short presentation about the tools that I use for my research in Cayenne, French Guiana (sickle, velvet, digital normalization (khmer), krona, awk and others).

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    Viral biodiversity in rodents Viral biodiversity in rodents Presentation Transcript

    • Does human perturbation affect the viral biodiversity of rodents? nacho caballero pasteur cayenne
    • Collect biological samples
    • Isolate the viruses
    • Sequence viral cDNA
    • Analyze read quality FastQC
    • Trim low-quality base pairs sickle - github.com/najoshi/sickle
    • Split reads into k-mers k
    • Remove redundant reads number of nucleotides with that coverage 0 10 coverage 100
    • Remove redundant reads digital normalization (khmer) number of nucleotides with that coverage 0 10 coverage 100
    • Assemble reads into contigs velvet - www.ebi.ac.uk/~zerbino/velvet/
    • Align contigs to known sequences blastn - blastx - tblastx NCBI bit.ly/vipr_download viprbrc.org
    • Classify alignments by taxonomy krona
    • zsh (globbing, renaming) awk sed join sort grep cut R Powerful file manager Small tools that do one thing well Statistics and data reshaping
    • Does human perturbation affect the viral biodiversity of rodents? nacho@bu.edu