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nlapier2 / Metalign

Metalign: efficient alignment-based metagenomic profiling via containment min hash
MIT License
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Can metalign be used for profiling (micro)eukaryotes? #13

Closed Anto007 closed 4 years ago

Anto007 commented 4 years ago

Can metalign be used for profiling (micro)eukaryotes in metagenomes? I believe the answer is "No" but I would appreciate if you could confirm this.

nlapier2 commented 4 years ago

Hi there, Metalign is capable of profiling single-celled eukaryotes. Of course, reference databases have fewer reference genomes for eukaryotes than for bacteria, so that has to be kept in mind.

Anto007 commented 4 years ago

Many thanks for your kind clarification. I'm curious to know why you chose to leave out plants and animals (esp. Homo sapiens; of course, I'm aware that it is best if human reads are filtered out prior to analysis)? For example, in clinical metagenomic libraries, it will be useful to know the relative abundance of reads from human and similarly, the relative abundance of plant pollen in environmental metagenomes

nlapier2 commented 4 years ago

That's an interesting point. We left them out because we only want to profile microorganisms, but I see how their inclusion could be relevant for some contexts. This is a feature we'll think about adding.