Introduction

This report documents the binning of a Nitrospira 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 2

The combination of the coverage of sample Gel1 and MBR1 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(1,15) +
  ylim(1,15)

#p
#sel <- mmplot_locator(p)

sel <- data.frame(Gel1  =  c(4.29, 6.05, 7.78, 8.41, 8.35, 6.17, 4.62, 4.02),
                  MBR1 = c(6.28, 7.83, 8.65, 7.63, 6.77, 5.3, 4.33, 5.02))

mmplot_selection(p, sel)