This report documents the binning of a Nitrospira genome from the GWW sample. See Daims et al., 2015: Complete Nitrification by Nitrospira Bacteria for further details.

Load the mmgenome package

The metagenome data is analysed using the mmgenome package.


Import data

The Rmarkdown file Load_data.Rmd describes the loading of the data and can be imported using the mmimport function. However, the preprocessed data can also be downloaded directly from figshare: Daims_GWW. Hence, here we import the prepocessed data from figshare instead.


Extract Nitrospira 10

As seen from the overview plots, there are numerous Nitrospira species. This one is located between multiple other species.

p <- mmplot(data = d,
            x = "HPD", 
            y = "HPF1", 
            log.x = T, 
            log.y = T, 
            color = "essential", 
            minlength = 5000) +
  scale_x_log10(limits=c(2, 30)) +
  scale_y_log10(limits=c(5, 50))

#sel <- mmplot_locator(p)

sel <- data.frame(HPD  =  c(5.86, 8.09, 12.2, 12.1, 8.67, 6.58, 5.56),
                  HPF1  =  c(13.2, 16.8, 18.9, 15.2, 11.7, 10.3, 10.6))

mmplot_selection(p, sel)