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 3

This Nitrospira seem to assemble very nicely. Hence, additional effort is done to obtain a clean genome bin.

p <- mmplot(data = d,
            x = "HPD", 
            y = "HPF1", 
            log.x = F, 
            log.y = F, 
            color = "essential", 
            minlength = 1000,
            factor.shape = "solid") +
  xlim(10, 50) +
  ylim(1, 7.5)

#p
#sel <- mmplot_locator(p)

sel <- data.frame(HPD  =  c(26.8, 27.5, 30.3, 38.9, 39.6, 35.8, 26.3),
                  HPF1  =  c(3.51, 2.85, 2.81, 3.72, 4.76, 5.9, 4.74))

mmplot_selection(p, sel)

The scaffolds included in the defined subspace are extracted using the mmextract function. One scaffold is excluded using network plots.

dA <- mmextract(d, sel, exclude = "47021")

The mmstats function applies to any extracted object. Hence, it can be used directly on the subset.

mmstats(dA, ncov = 2)
##               General Stats
## n.scaffolds           49.00
## GC.mean               55.80
## N50               155638.00
## Length.total     3443025.00
## Length.max        320146.00
## Length.mean        70265.80
## Coverage.HPD          33.75
## Coverage.HPF1          4.15
## Ess.total             91.00
## Ess.unique            90.00

Subset B

Unsing PE reads.

dB <- m