A 16S pipeline for a reference-based local alignment of 16S sequences to the reference database RExMapDB of known isolate microbial strains.
For Linux, we need to make sure you have development version of OpenSSL installed, so e.g. for Ubuntu run from terminal:
sudo apt-get -y install libssl-dev libcurl4-openssl-dev
Then to install the latest version of R, we need to add the repository, authentication key and install it:
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb [arch=amd64,i386] https://cran.rstudio.com/bin/linux/ubuntu xenial/'
sudo apt-get update
sudo apt-get -y install r-base
In R, install devtools package, then use install_github to install the package from source:
install.packages('devtools')
devtools::install_github('benjjneb/dada2')
# Select 1 when prompted to install biocLite
devtools::install_github('sapientbio/rexmap-open')This may take up to about 10 minutes to install on a fresh R installation.
First, make sure you have the latest Xcode and latest R (> 3.4) installed. Then, install Xcode command line tools. To do this, open a macOS Terminal, then type
xcode-select --install
Then open either R console or RStudio and run this:
# Install devtools first
options('install.packages.compile.from.source'='never')
install.packages('devtools')
# DADA2 pre-requisites
source('http://bioconductor.org/biocLite.R')
biocLite('GenomeInfoDbData', suppressUpdates=T)
# DADA2
devtools::install_github('benjjneb/dada2')
# Finally install RExMap
devtools::install_github('sapientbio/rexmap-open')- Human gut microbiome data tutorial (main tutorial with all explanations)
- mock community tutorial
By default, multithreading is enabled and supported only on Linux and macOS, through R package parallel.
If DADA2 package installation fails due to latticeExtra package requiring R version 3.6 and you are running 3.5, you can use this to install an older version of the latticeExtra package:
devtools::install_version('latticeExtra', version='0.6-28', repos='http://cran.us.r-project.org')RExMap is provided under the Attribution-NonCommercial-ShareAlike 4.0 International license.