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.

• Version: 0.5.0
• Added: January, 2023
• Link: https://github.com/bx3/shannon_cpp

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.