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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](Appendix.\ Input\ file\ formats) 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:

• R - R Core Team. 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. (http://www.R-project.org/)
• BBMap - Bushnell B. 2015. BBMap (http://sourceforge.net/projects/bbmap/)
• AMPHORA2 - Wu M, Scott AJ. 2012. Bioinformatics 28 (7) : 1033-1034.
• barrnap - Seemann T. 2014. barrnap (http://www.vicbioinformatics.com/software.barrnap.shtml)
• Usearch - Edgar RC 2010. Bioinformatics 26 (19) : 2460-2461.
• Vsearch - https://github.com/torognes/vsearch
• ARB-SILVA - Quast C et al. 2013. Nucleic Acids Research 41 (D1) : D590-D596.
• tRNAscan-SE - Lowe T, Eddy S. 1997. Nucleic Acids Research 25 : 955-964.
• Blobology - Kumar S et al. 2013. Frontiers in Genetics 4 : 237

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

First step...

Read the introduction