Introduction

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.

library("mmgenome")

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.

load("Daims_GWW.RData")

Extract Nitrospira 9

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, 
            factor.shape = "solid") +
  scale_x_log10(limits=c(2, 30)) +
  scale_y_log10(limits=c(5, 50))

#p
#sel <- mmplot_locator(p)

sel <- data.frame(HPD  =  c(9.24, 9.46, 13.1, 18, 23.7, 18.2, 11.1, 9.14),
                  HPF1  =  c(11.3, 9.72, 9.24, 11.6, 18.3, 20.1, 14, 11.4))

mmplot_selection(p, sel)