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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
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Can this atlas analyze human metagenome? #548

Closed luozhy88 closed 2 years ago

luozhy88 commented 2 years ago

Can this atlas analyze human metagenome? Can the metagenome of human feces be analyzed by atlas?

SilasK commented 2 years ago

Yes, you can. I did it and many others do. If you do don't forget to add the human genome as a decontamination reference, as described in the docs.

However, I would say there are already good reference databases for the human gut, at least for Europe + US. Because there are already many groups that assembled genomes from the human gut.

Therefore, If your main goal is simply to get the abundance of bacteria in human samples, there are other tools for doing this quickly.

For example, I created a pipeline using the unified human gut genomes. I also have the annotation of Kegg modules and other functional genes, which allows you simply calculate their abundances. More info here: https://github.com/SilasK/Krak

But if you want to do something else, that needs assembly, yes you can use atlas.

luozhy88 commented 2 years ago

If I want to add a command about in the config "hsa: /data2/zhiyu/database/sunbeam/host_hsa/Homo_sapiens.GRCh38.dna.primary_assembly.fa", right?

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SilasK commented 2 years ago

Yes.

luozhy88 commented 2 years ago

Because I changed the samples.tsv file, and save as samles_new.tsv . can I specify its absolute path? atlas run qc --samples /home/zhiyu/atlas/samles_new.tsv ,right?

luozhy88 commented 2 years ago

Help!