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...
Does human perturbation affect the viral biodiversity of rodents? nacho@bu.edu
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).

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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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