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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
$ 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 /export/apps/shannon_cpp/0.5.0/bin

Also see the bioconda recipe for shannon_cpp.

shannon_cpp-software.txt · Last modified: 2023/01/24 14:09 by aorth