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 2

The second Nitrospira bin can also be relatively easy seperated from the other genomes.

p <- mmplot(data = d, 
            x = "HPD", 
            y = "HPF1", 
            log.x = F, 
            log.y = F, 
            color = "essential", 
            minlength = 1000,
            factor.shape = "solid") +
  xlim(0, 50) +
  ylim(50, 600)

#p
#sel <- mmplot_locator(p)

sel <- data.frame(HPD  =  c(-0.483, 0.487, 12.9, 25.5, 23.4, 11.7, 2.75),
                  HPF1  =  c(210, 292, 307, 292, 209, 148, 148))

mmplot_selection(p, sel)