nacho caballero pasteur cayenne

Does human perturbation affect the viral biodiversity of rodents?

Collect biological samples

Isolate the viruses

Sequence viral cDNA

FastQC

Analyze read quality

sickle - github.com/najoshi/sickle

Trim low-quality base pairs

k

Split reads into k-mers

Remove redundant reads

0coverage

10

number of nucleotides

with that coverage

100

Remove redundant reads

coverage0 10 100

digital normalization (khmer)number of

nucleotides with that coverage

Assemble reads into contigs

velvet - www.ebi.ac.uk/~zerbino/velvet/

Align contigs to known sequences

blastn - blastx - tblastx

NCBI

viprbrc.orgbit.ly/vipr_download

Classify alignments by taxonomy

krona

Small tools that do one thing well

awk sed join sort grep cut

Powerful file manager

zsh (globbing, renaming)

Statistics and data reshaping

R

Does human perturbation affect the viral biodiversity of rodents?

nacho@bu.edu