We are in the process of finalizing a new major release of salmon, and are looking for people willing to test the latest (beta) releases and give feedback. Though the command-line interface is largely identical to the current version, the forthcoming release makes use of a different and much more compact index than previous versions. This makes it possible to index much larger collections of reference sequence with moderate memory, allows the use of more comprehensive decoy sequence, and speeds up the loading of indices for large references. Further, the new version adopts an improved selective-alignment algorithm. This release also contains a number of other smaller improvements and bug fixes documented in the current beta release notes.
In addition to the immediate benefits, the ability to include considerably more sequence in the index opens up the door to interesting new features that are currently being explored. However, since the forthcoming update constitutes such a change, we will be doing a major version bump, and are making a few beta releases until a wider scope of users have had a chance to try it out and provide feedback; so please give it a try if you have a chance.