Installation

SSUnique is designed to run in a Linux environment and was developed and tested in Ubuntu 14.04 LTS and 16.04 LTS. It has additionally been tested and is functional in Mac OSX. The scripts used in SSUnique can be cloned or downloaded directly from the repository. To clone the SSUnique scripts and test data, in a directory of your choosing on your local system, run:

git clone https://github.com/neufeld/SSUnique.git
cd SSUnique

The pipeline has several software dependencies to be fully functional:

• [FastTree] (http://www.microbesonline.org/fasttree) (tested with v. 2.1.3 SSE3)
• [infernal] (http://eddylab.org/infernal/) (tested with v. 1.1.1)
• [ssualign] (http://eddylab.org/software/ssu-align/) (tested with v. 0.1.1)
• [base R] (https://www.r-project.org/) (R >= v. 3.2)
• [HMMER] (http://hmmer.org/) (v. 3.1)

These can each be installed manually or using the base_check.sh install script in the repository (https://github.com/neufeld/SSUnique). Depending on your setup you may need to use the sudo command with the base_check.sh script (note that you may be asked to confirm yes/no before installing each dependency):

chmod u+x base_check.sh
./base_check.sh 

Additionally, several R packages are required. These packages are installed/loaded when running SSUnique, but can be installed independently within R instructions and Bioconductor (Biostrings, phyloseq) instructions.

• [ape] (https://cran.r-project.org/web/packages/ape/index.html)
• [biom] (https://cran.r-project.org/web/packages/biom/index.html)
• [optparse] (https://cran.r-project.org/web/packages/optparse/index.html)
• [ggplot2] (https://cran.r-project.org/web/packages/ggplot2/index.html)
• [reshape] (https://cran.r-project.org/web/packages/reshape/index.html)
• [pacman] (https://cran.r-project.org/web/packages/pacman/index.html)
• [Biostrings] (https://bioconductor.org/packages/release/bioc/html/Biostrings.html)
• [phyloseq] (https://bioconductor.org/packages/release/bioc/html/phyloseq.html)

SSUnique merges unclassified sequences with a reference data set in order to provide a phylogenetic placement of those unclassified OTU sequences. This reference data set can be any set of sequences aligned by infernal. By default, SSUnique can download and prepare SILVA Living Tree Project reference data for general use in bacterial 16S rRNA gene amplicon studies. Again, depending on your setup you may need to use the sudo command with the reference_data.sh script:

chmod u+x reference_data.sh
./reference_data.sh