Comparing metagenome profiles with publicly available profiles from sandpiper

wwood / singlem

Novelty-inclusive microbial community profiling of shotgun metagenomes

http://wwood.github.io/singlem/

GNU General Public License v3.0

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Comparing metagenome profiles with publicly available profiles from sandpiper #192

Open adityabandla opened 1 month ago

adityabandla commented 1 month ago

Dear Ben,

I am interested in comparing my metagenomes to a number of samples from the same biome that are publicly available. My comparison would be in the form of beta diversity estimates and the approach would be to (i) pick a subset of markers, (ii) combine otu tables from my metagenomes with the ones from sandpiper, and (iii) calculate beta diversity and check for concordance among markers. Would this approach be valid?

Regards, Adi

wwood commented 1 month ago

Hi, This seems reasonable. One thing to watch for is that only some of the markers target both Bacteria and Archaea - it might be best to stick to these ones. You can tell which is which using singlem metapackage --describe.