viral biodiversity in rodents
DESCRIPTION
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).TRANSCRIPT
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
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
