Introduction

This report documents the binning of a Nitrospira Commamox genome from a full-scale wastewater treatment plant (VetMed). 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_VetMed. Hence, here we import the prepocessed data from figshare instead.

load("Daims_VetMed.RData")

Extract Nitrospira

Subset A

The combination of the coverage of sample VM23 and VMPS are used to make an intial extraction that includes the Nitrospira genome.

p <- mmplot(data = d, 
            x = "VM23", 
            y = "VMPS", 
            color = "essential", 
            minlength = 5000,
            factor.shape = "solid") +
  xlim(0,20) +
  ylim(0,5)

#p
#sel <- mmplot_locator(p)

sel <- data.frame(VM23  =  c(8.75, 10.1, 15.2, 18.5, 18.9, 16.3, 11),
                  VMPS  =  c(1.67, 2.44, 2.94, 2.74, 1.83, 1.07, 1.06))

mmplot_selection(p, sel)