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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