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kbseah edited this page Jan 4, 2016 · 8 revisions

gbtools: Interactive metagenome visualization and binning in R

Read the paper: Seah BK and Gruber-Vodicka HR (2015). gbtools: Interactive visualization of metagenome bins in R. Front. Microbiol. 6:1451.

Quick start

Assuming you already have metagenomes assembled, coverage calculated by mapping, marker genes identified and taxonomically classified. What next?

  • Download the latest release of gbtools
  • Install package dependencies in R (sp and plyr packages)
  • Install gbtools package in R
  • Format input data, and check with input_validator.pl (in the accessory_scripts folder)
  • Load your data into R: A <- gbt(covstats=c("coverage_file1.tab","coverage_file2.tab"),mark="taxonomic_markers.tab",marksource="source",ssu="ssu_markers.tab",trna="trna_markers.tab")
  • Plot GC-coverage plots: plot(A, slice=1)
  • Select contigs by coverage/gc/length cutoffs: A.bin1 <- winnow(A,gc=c(0.25,0.35),len=c(10000,Inf),covmin=100,covmax=Inf,slice=1)
  • Overlay bin on plot: points(A.bin1,slice=1)
  • Plot differential-coverage plot: plot(A,slice=c(1,2))
  • Overlay bin on differential coverage plot: points(A.bin1, slice=c(1,2))
  • Choose bin by interactively selecting a cloud of points on plot: A.bin2 <- choosebin(A, slice=c(1,2))
  • View summary statistics for a bin: summary(A.bin2)

Getting help

Problems with using gbtools? Create a new issue using the GitHub issue-tracker on the right. Or send me an email, with "gbtools help" in the subject line.

Problems with input file formats? Read the appendix and use the input_validator.pl script to check your input files.

Citations

Citation: Seah BK and Gruber-Vodicka HR (2015). gbtools: Interactive visualization of metagenome bins in R. Front. Microbiol. 6:1451. doi: 10.3389/fmicb.2015.01451

Cite dependencies if you use them:

Contact: Brandon Seah (kbseah@mpi-bremen.de)

First step...

Read the introduction