Shannon is a novel de novo RNA-Seq assembler designed based on information-theoretic principles.
We develop its C++ implementation here, which significantly improves both time and memory efficiency by an order of magnitude than its original (currently deprecated) Python prototype.
See versions which are available:
$ module avail shannon_cpp
Load one version into your environment and run it:
$ module load shannon_cpp/0.5.0 $ shannon_cpp
Notes from the sysadmin during installation:
$ cd /tmp $ wget https://github.com/bx3/shannon_cpp/releases/download/v0.5.0/shannon-source-v0.5.0.tar.gz $ tar xf shannon-source-v0.5.0.tar.gz $ cd shannon-source-v0.5.0 $ sudo dnf install metis-devel.x86_64 glpk-devel.x86_64 sparsehash-devel.x86_64 $ cmake . $ make -j4 $ sudo mkdir -p /export/apps/shannon_cpp/0.5.0/bin $ sudo cp shannon_cpp run_batch.py syrupy.py /export/apps/shannon_cpp/0.5.0/bin
Also see the bioconda recipe for shannon_cpp.