Shannon is a program for assembling transcripts from RNA-Seq data. It is based on an information-theoretic approach to assembly that seeks to establish both necessary and sufficient conditions for optimal assembly as well as algorithms for achieving optimal assembly.

Shannon is a collaborative effort between three universities: Sreeram Kannan at University of Washington, Lior Pachter at University of California, Berkeley and David Tse at Stanford University. The programming of Shannon was led by Sreeram Kannan and carried out by Joseph Hui and Kayvon Mazooji.

Shannon was partially funded by the NSF Center for Science of Information, NIH NHGRI and a startup grant at the University of Washington.