Question: Viral mapping of new strains within host samples
gravatar for ehodzic
3.7 years ago by
United States
ehodzic10 wrote:

We have conducted NGS run on Ion Torrent looking for presence of unknown viruses within host samples. We would like to built a reference genome from all viral nucleotides available in genbank to conduct mapping of our runs. I was wondering if we can do that on Galaxy, what tools to use, and how to do it?

Thank you,


mapping viral galaxy • 769 views
ADD COMMENTlink modified 3.7 years ago by Martin Čech ♦♦ 4.9k • written 3.7 years ago by ehodzic10
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Genbank is a great source for this data.

You could use Genbank's WGS database (currently used with Megablast on Main http://usegalaxy) and filter the results phylogenically. 

Best, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
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