1.
Does human
perturbation
affect the
viral biodiversity
of rodents?
nacho caballero
pasteur cayenne

2.
Collect biological samples

3.
Isolate the
viruses

4.
Sequence viral cDNA

5.
Analyze read quality
FastQC

6.
Trim low-quality base pairs
sickle - github.com/najoshi/sickle

7.
Split reads into k-mers
k

8.
Remove redundant reads
number of
nucleotides
with that
coverage
0
10
coverage
100

9.
Remove redundant reads
digital normalization
(khmer)
number of
nucleotides
with that
coverage
0
10
coverage
100

10.
Assemble reads into contigs
velvet - www.ebi.ac.uk/~zerbino/velvet/

11.
Align contigs to known sequences
blastn - blastx - tblastx
NCBI
bit.ly/vipr_download
viprbrc.org

12.
Classify alignments by taxonomy
krona

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