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mmgenome: a toolbox for reproducible genome extraction from metagenomes

By Søren M Karst, Rasmus H Kirkegaard, Mads Plesner Albertsen

Posted 15 Jun 2016
bioRxiv DOI: 10.1101/059121

Recovery of population genomes is becoming a standard analysis in metagenomics and a multitude of different approaches exists. However, the workflows are complex, requiring data generation, binning, validation and finishing to generate high quality population genome bins. In addition, several different approaches are often used on the same dataset as the optimal strategy to extract a specific population genome varies. Here we introduce mmgenome: a toolbox for reproducible genome extraction from metagenomes. At the core of mmgenome is an R package that facilitates effortless integration of different binning strategies by collecting information on scaffolds. Genome binning is facilitated through integrated tools that support effortless visualizations, validation and calculation of key statistics. Full reproducibility and transparency is ob-tained through Rmarkdown, whereby every step can be recreated.

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