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).

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Viral biodiversity in rodents

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

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