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We implemented a bioinformatics workflow (Agnostos) to structure and explore the large pool of genes with unknown functions found in microbial genomes and metagenomes. We used a protein domain-based approach to partition more than 400 million predicted genes from 1,628 metagenomes and ~29 genomes into different categories of gene clusters of known and unknown functions.

<img alt="workflow.png" src="img/workflow.png" width="750" height="" >

<a name="wrkfl"></a>_Agnostos workflow different modules_

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The AGNOSTOS WORKFLOW can be found [HERE](https://github.com/functional-dark-side/agnostos-wf).

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The methods (included all the scripts/code) and results for each module are documented. Below you can find the links to the different reports:

[**DATA**](1_Data)


<h3 class="section-heading  text-primary">Workflow steps</h3>


-   [1. Gene prediction](2_Gene_prediction)
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-   [2. MMseqs clustering](3_MMseqs_clustering)
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-   [3. Pfam annotations](4_Pfam_annotation)
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-   [4. Cluster validation](5_Cluster_validation)
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-   [5. Cluster refinement](6_Cluster_refinement)
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-   [6. Cluster classification in categories](7_Cluster_classification)
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-   [7. Known-Unknown cluster category refinement](8_Known-Unknown_refinement)
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-   [8. Cluster communities inference](9_Cluster_communities)

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**Main analyses and results:**

-   [**Cluster and communities overview**](17.1_Cluster_and_communities_overview)

-   [**Coverage of external databases**](10_Coverage_external_DBs)

-   [**EUs in MAGs**](11_EUs_MAGs)

-   [**GTDB genomes integration**](12_GTDB_genome_integration)

-   [**Environmental analyses**](13_Environmental_analyses)

-   [**Phylogenomic analyses**](14_Phylogenomic_analyses)

-   [**TARA ocean OM-RGC-v.2 integration**](15_Tara_Ocean_OMRGCv2)

-   [**Mutant phenotypes**](16_Mutant_phenotypes)

-   [**Results in numbers**](17_Cluster_DB_numbers)

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