PT  - JOURNAL ARTICLE
AU  - Søeren M. Karst
AU  - Rasmus H. Kirkegaard
AU  - Mads Albertsen
TI  - mmgenome: a toolbox for reproducible genome extraction from metagenomes
AID  - 10.1101/059121
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 059121
4099  - http://biorxiv.org/content/early/2016/06/15/059121.short
4100  - http://biorxiv.org/content/early/2016/06/15/059121.full
AB  - Summary 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 obtained through Rmarkdown, whereby every step can be recreated.Availability and implementation The binning framework of mmge-nome is implemented in R. Wrapper scripts for data generation and finishing is written in Perl. The mmgenome toolbox and associated step-by-step guides are available at http://madsal-bertsen.github.io/mmgenome/.Contact ma{at}bio.aau.dkSupplementary information Supplementary data are available at Bioinformatics online.