How to dereplicate MAGs? (metagenome assembly genomes)

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Bioinformatics metagenomics microbiology Assembly microbial-genomes

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  • drep

    Rapid comparison and dereplication of genomes (by MrOlm)

    • You should look at https://github.com/MrOlm/drep . Thats exactly the tool you need. Usually one takes all their bins and dereplicates them at 99% ANI for strain level dereplication or 95% at species level. For preserving the best quality, you would need to check yourself if the best genome survived the dereplication afaik. You probably want some sort of quality score and chose the one with the highest score out of the bins that got grouped as one by dereplication.

  • DAS_Tool

    DAS Tool

    • I always use DAS_Tool to get the best possible set of bins https://github.com/cmks/DAS_Tool

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