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title: Genomes collection
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---
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At this stage of the workflow, we have a number of bins obtained from the assembly of sample reads. The next step is to check the quality of this bins, then obtain their abundance and annotate them functionally and taxonomically.
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- [ABRicate](https://github.com/tseemann/abricate) : Enables mass screening of contigs for antimicrobial resistance or virulence genes
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- [AMRFinderPlus](https://github.com/ncbi/amr) : a tool designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences
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A tool for the detection of MGEs (Mobile Genetic Elements) have also been added with [genomad](https://github.com/apcamargo/genomad) to identify viruses and plasmids in the MAGs. The tool can be used in the genomes collection but also in the [genes collection](genes_collection) part in a complementary way.
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### Genomes taxonomic annotation ###
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Taxonomic annotation of MAGs is performed using [GTDB-tk](https://github.com/Ecogenomics/GTDBTk), which allows taxonomic information to be assigned to each MAG.
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