Assess the ability to detect viruses

knights-lab / analysis_SHOGUN

Analysis scripts and code for reproducing the analysis for the SHOGUN paper

MIT License

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Open bhillmann opened 7 years ago

bhillmann commented 7 years ago

[x] Assess virome recovery
[x] Find out how deep you have to sequence human stool to get good recall of viruses (based on comparisons to deep shotgun)

RRShieldsCutler commented 7 years ago

Sounds like we need a virome.ctr shogun database. There's gotta be a refseq virus set or something...

bhillmann commented 7 years ago

This is accessible for sure.

bhillmann commented 7 years ago

Can you give me write access to:

/project/flatiron2/ben/projects/analysis_SHOGUN/detect_viruses

RRShieldsCutler commented 7 years ago

Ok, you should have access now.

bhillmann commented 7 years ago

Can you rerun this with the confidence UTree version? Then we should be done.

RRShieldsCutler commented 7 years ago

Running currently. Should finish this evening sometime. I'll update with the result when it finishes.

RRShieldsCutler commented 7 years ago

Finished, results here:

/project/flatiron2/ben/projects/analysis_SHOGUN/detect_viruses/results/karlsson161205/shogun_utree_lca_out/