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 7

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 = 1000,
            factor.shape = "solid") +
  scale_x_log10(limits=c(20, 120)) +
  scale_y_log10(limits=c(20, 100))

#p
#sel <- mmplot_locator(p)

sel <- data.frame(HPD  =  c(52.6, 61.4, 44.5, 30.9, 31, 42),
                  HPF1  =  c(38.3, 31.6, 21.7, 22.2, 27, 36.2))

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         1371.00
## GC.mean               56.40
## N50                 7982.00
## Length.total     6574813.00
## Length.max         77984.00
## Length.mean         4795.60
## Coverage.HPD          43.08
## Coverage.HPF1         28.63
## Ess.total            123.00
## Ess.unique            81.00
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(-0.0642, -0.0416, 0.0582, 0.124, 0.0397, -0.0457),
                  PC2  =  c(-0.0662, -0.0105, -0.0387, -0.0962, -0.196, -0.166))

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         1095.00
## GC.mean               57.70
## N50                 9145.00
## Length.total     5817263.00
## Length.max         77984.00
## Length.mean         5312.60
## Coverage.HPD          43.07
## Coverage.HPF1         28.48
## Ess.total            108.00
## Ess.unique            76.00

Export the scaffolds

Finally the binned scaffolds are exported.

mmexport(data = dB, assembly = assembly, file = "GWW_Nitrospira7.fa")