Question: Viral mapping of new strains within host samples
1
gravatar for ehodzic
3.0 years ago by
ehodzic10
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,

Emir 

mapping viral galaxy • 587 views
ADD COMMENTlink modified 2.9 years ago by Martin Čech ♦♦ 4.3k • written 3.0 years ago by ehodzic10
0
gravatar for Jennifer Hillman Jackson
3.0 years ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink written 3.0 years ago by Jennifer Hillman Jackson24k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 85 users visited in the last hour