Analysis of Double Barcoded Illumina Amplicon Data
Minimum requirements for the dbcAmplicons package: Python 2.X is required to run any and all of the elements in the package. Some applications within the package rely on FLASH or the RDP classifier to complete, so the user must determine of those external tools are necessary if the entire pipeline will not be run.
External programs used in the pipeline:
- FLASH2 (https://github.com/dstreett/FLASH2)
- RDP classifier (https://github.com/rdpstaff/RDPTools)
- bowtie2 (https://github.com/BenLangmead/bowtie2)
dbcAmplicons has not been tested on Windows systems, although Windows Powershell (active in XP systems and later) may be sufficient to run the analysis. It is highly recommended, however, that the user install a Linux-based virtual machine to run the pipeline.
Mac users should first download and install Xcode and then download the app via a terminal by:
git clone https://github.com/msettles/dbcAmplicons.git
cd dbcAmplicons
python setup.py install
dbcAmpliconsIf installation was successful, this will bring up the usage arguments.
For Linux users, some python dependencies may be required before the installation is succesful. To install, open a terminal and type
sudo apt-get install python-dev
sudo apt-get install numpyAnd type the sudo password at the prompt. Then, download the app via a terminal by:
git clone https://github.com/msettles/dbcAmplicons.git
cd dbcAmplicons
sudo python setup.py install
dbcAmpliconsIf installation was successful, this will bring up the usage arguments.