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Question from a user:
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Replies: 2 comments
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Hello, It is true the main usage of atlas is to generate MAGs of a dataset. You are afraid that you will not be able to produce high-quality bins from your dataset, whichz is understadable. Some metagenomes are difficult. Just to keep in mind that atlas creates a non-redundant set of MAGs (one per species). So you only would need 1 good quality genome per species from any of your samples. So for many metagenome this should be worth to try how many reads are mapped with the MAG aproach
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However the good news is even if you don't get anough MAGs, there is the genecatalog workflow For now, the genecatalog is annotated using eggNOG mapper. WggNOG mapper has some links to Kegg. This should be ok to calculate a functional richness/diversity. |
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However the good news is even if you don't get anough MAGs, there is the genecatalog workflow
atlas run genecatalog
It produces a non redundant set of all genes infered from a assembly. This should be what you are looking for.For now, the genecatalog is annotated using eggNOG mapper. WggNOG mapper has some links to Kegg. This should be ok to calculate a functional richness/diversity.
But we are also planning to annotat the genecatlaog directly with the KOfams.