Introduction

This report documents the binning of a Nitrospira Comammox genome from a pilot-scale MBR reactor used for wastewater treatment (MBR). 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_MBR. Hence, here we import the prepocessed data from figshare instead.

load("Daims_MBR.RData")

Extract Nitrospira 1

The combination of the coverage of sample Gel1 and MBR are used to make an intial extraction that includes the Nitrospira genome.

p <- mmplot(data = d, 
            x = "Gel1", 
            y = "MBR1", 
            log.x = F, 
            log.y = F, 
            color = "essential", 
            minlength = 5000,
            factor.shape = "solid") +
  xlim(5,25) +
  ylim(1,15)

#p
#sel <- mmplot_locator(p)

sel <- data.frame(Gel1  =  c(8.64, 12.6, 16, 18, 15.1, 10.6, 8.27),
                  MBR1  =  c(5.7, 8.63, 9.72, 8.93, 6.24, 4.67, 4.48))

mmplot_selection(p, sel)