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Question: Viral mapping of new strains within host samples
1
gravatar for ehodzic
3.7 years ago by
ehodzic • 10
United States
ehodzic • 10 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,

Emir 
mapping viral galaxy • 769 views
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modified 3.7 years ago by Martin Čech ♦♦ 4.9k • written 3.7 years ago by ehodzic • 10
0
gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Genbank is a great source for this data.
http://www.ncbi.nlm.nih.gov/genomes/GenomesGroup.cgi?taxid=10239

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 COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
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