(cross-posted on seqanswers a few days ago --- http://seqanswers.com/forums/showthread.php?t=49062, please let me know if posting here now is a violation of etiquette!)
I'd like to let you know about Salmon, a new tool we've been developing for isoform-level quantification from RNA-seq data. It is, conceptually, the successor to our Sailfish software, but boasts a significant number of improvements and relies on a very different methodology. It maintains or improves upon the main strengths of Sailfish (i.e. it is as-fast to faster in most situations, and requires substantially less memory --- especially for large transcriptomes) while providing a number of additional benefits. For example, it eliminates the need to build a parameter-dependent (k-mer size) index, and makes much better use of paired-end data and longer reads --- in the testing we and others have done so far, it appears to be very accurate even in complex situations. It also provides alignment-based and alignment-free quantification modes to suit users with both needs.
Salmon is fully open source, and is currently being developed on the develop branch of the Sailfish GitHub repository. The documentation is available via ReadTheDocs, the latest binaries are available here, and we welcome questions and discussion on the Sailfish Google Group. The manuscript is in preparation, but we already have a number of people testing and using the software, and we'd like to get input and feedback from the community as we finish the manuscript. So please, give salmon a try --- it's tasty ;).