Cliffy is software tool that utilizes a novel data-structure for document listing called document array profiles in order to classify sequencing reads. Cliffy is capable of taxonomic classification (classification w.r.t to a tree) and multi-class classification.
Currently, the only way to install Cliffy is by installing from the GitHub repo. Instructions are shown below. We are working on creating a Docker container as well as including it as a bioconda package.
In the wiki-page for this repo, we go through two different possible use-cases for Cliffy using data given in the repo. The first one is a multi-class classification scenario with 4 different genomes. And the second is performing taxonomic classification of 16S rRNA reads against the SILVA database.
- Example 1: Multi-class classification of Bacillus reads
- Example 2: Taxonomic classification of 16S rRNA reads
Follow the instructions in the wiki after installation, and write a GitHub issue if you have any questions/problems!
For starting out, use the commands below to download the repository and build the executable. After running the make command below,
the pfp_doc executable will be found in the build/ folder.
git clone [email protected]:oma219/docprofiles.git
cd docprofiles
mkdir build
cd build && cmake ..
make install
export PFPDOC_BUILD_DIR=$(pwd)