====== shannon_cpp ======
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.

===== Information =====

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

===== Usage =====

See versions which are available:
<code>$ module avail shannon_cpp</code>

Load one version into your environment and run it:

<code>$ module load shannon_cpp/0.5.0
$ shannon_cpp</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ 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</code>

Also see the [[https://github.com/bioconda/bioconda-recipes/tree/master/recipes/shannon_cpp|bioconda recipe for shannon_cpp]].