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