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CAMI-challenge / OPAL

OPAL: Open-community Profiling Assessment tooL
https://cami-challenge.github.io/OPAL/
Apache License 2.0
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assessment on CAMI data #17

Closed alicemchardy closed 6 years ago

alicemchardy commented 6 years ago

compare all results with CAMI to make sure metrics are in good shape

alicemchardy commented 6 years ago

david koslicki will run some of these tools, crearte a wrapper opal output, generate results for opal paper, once opal output is ready.

-downstream relevance : tools can be put into bioboxes; maybe wait a bit since tools might be still in development and improve a bit..

dkoslicki commented 6 years ago

I intend to write wrappers for SourMash, CMash, and Mash-screen. I will then apply these tools on the CAMI data.

It should be noted that as of yet, only SouMash reports relative abundances (which are a kind of modified relative abundance), so some of the diversity-related metrics won't be applicable. This shouldn't be an issue as I foresee only including these results for sensitivity/specificity related metrics.

abremges commented 6 years ago

@fernandomeyer will dive into it 👍

abremges commented 6 years ago

And @dkoslicki, as outlined above (sorry).

dkoslicki commented 6 years ago

I've gotten these tools (sourmash, CMash, Mash-screen) to run on the CAMI data, but due to grant stuff, will not be able to get to writing wrappers until 1.5+ weeks from now.

fernandomeyer commented 6 years ago

Assessment on CAMI high challenge is being demonstrated in the manuscript.