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| # Welcome to MAGset | ||
| MAGset is a tool to analyze genomes obtained from metagenomic data (MAGs) of known species (which have published reference genomes). | ||
| <h1>Welcome to the MAGset wiki!</h1> | ||
| MAGset is a tool to analyze genomes obtained from metagenomic data (MAGs) of known species (which have published reference genomes).<br/><br/> | ||
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| Please open the Wiki (https://github.com/LaboratorioBioinformatica/MAGset/blob/master/wiki/README.md) for more information | ||
| The main goal is to find the differences between the genomes and identify the genomic regions of interest (GRIs) that exist in the MAG but don't exist in any reference genome (positive GRIs) and genomic regions of interest that exist in one or more reference genomes, but they don't exist in the MAG (negative GRIs). Negative GRIs can be caused by assembly errors, and using the MAGcheck module you can search for them in your raw data. | ||
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| <p>The tool generates the following results:</p> | ||
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| * ANI matrix between genomes; | ||
| * Pangenome (specific, shared and core genes); | ||
| * Identification of genomic regions of interest (GRIs); | ||
| * COGs and CAZy annotations; | ||
| * Advanced search of genes by gene data; | ||
| * Validation of MAG assembly using raw data vs references genomes; | ||
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| <p>All results are generated in HTML.</p> | ||
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| **MAgset Pipeline:** | ||
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| **Screenshot from a MAGset result:** | ||
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| <p>Please use the links below to learn more about the MAGset: </p> | ||
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| * [How to install](/wiki/How-to-install.md) | ||
| * [Quick start](/wiki/Quick-start.md) | ||
| * [What is Genomic Regions of Interest (GRIs)?](/wiki/Genomic-Region-Of-Interest.md) | ||
| * [Tutorial - GBFF files as input](/wiki/tutorial-gbff-files-as-input.md) | ||
| * [Tutorial - How to use the advanced gene search](/wiki/tutorial-advanced-gene-search.md) | ||
| * [Tutorial - Using MAGcheck](/wiki/tutorial-using-magcheck.md) | ||
| * [Input files](/wiki/Input-files.md) | ||
| * [Output files](/wiki/Output-files.md) | ||
| * [Parameters](/wiki/Parameters.md) | ||
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| ## Acknowledgements | ||
| This project was funded in part by [CNPq](https://www.gov.br/cnpq/pt-br), grant number 440230/2022-5, within the Call CNPq/MCTI/CT-Biotec number 30/2022 | ||
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| ## Article / How to cite | ||
| Coming soon! |