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 10

As seen from the overview plots, there are numerous Nitrospira species. This one is located between multiple other species.

p <- mmplot(data = d,
            x = "HPD", 
            y = "HPF1", 
            log.x = T, 
            log.y = T, 
            color = "essential", 
            minlength = 5000) +
  scale_x_log10(limits=c(2, 30)) +
  scale_y_log10(limits=c(5, 50))

#p
#sel <- mmplot_locator(p)

sel <- data.frame(HPD  =  c(5.86, 8.09, 12.2, 12.1, 8.67, 6.58, 5.56),
                  HPF1  =  c(13.2, 16.8, 18.9, 15.2, 11.7, 10.3, 10.6))

mmplot_selection(p, sel)

The scaffolds included in the defined subspace are extracted using the mmextract function.

dA <- mmextract(d, sel)

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         1658.00
## GC.mean               58.70
## N50                 8743.00
## Length.total     9416619.00
## Length.max         89856.00
## Length.mean         5679.50
## Coverage.HPD           8.35
## Coverage.HPF1         13.74
## Ess.total            140.00
## Ess.unique            93.00
mmplot_pairs(data = dA, 
             variables = c("HPD", "HPF1","gc", "PC1", "PC2", "PC3"), 
             minlength = 5000, 
             color = "essential")

Clean-up other species (Subset B)

We do a another selection to remove other Nitrospira scaffolds that were included.

p <- mmplot(data = dA,
            x = "PC1", 
            y = "PC2", 
            color = "essential", 
            minlength = 1000)

#p
#sel <- mmplot_locator(p)

sel <- data.frame(PC1  =  c(-0.0397, -0.00947, 0.05, 0.118, 0.0716, 0.00751),
                  PC2  =  c(-0.11, -0.212, -0.215, -0.121, -0.0417, -0.0626))

mmplot_selection(p, sel)

The scaffolds included in the defined subspace are extracted using the mmextract function.

dB <- mmextract(dA, sel)

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

mmstats(dB, ncov = 2)
##               General Stats
## n.scaffolds          846.00
## GC.mean               55.50
## N50                 5457.00
## Length.total     3369566.00
## Length.max         22477.00
## Length.mean         3982.90
## Coverage.HPD           8.21
## Coverage.HPF1         13.59
## Ess.total             15.00
## Ess.unique            15.00

Export the scaffolds

Finally the binned scaffolds are exported.

mmexport(data = dB, assembly = assembly, file = "GWW_Nitrospira10.fa")