Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves is accuracy and speed via a number of different innovations, including the use of quasi-mapping (accurate but fast-to-compute proxies for traditional read alignments), and massively-parallel stochastic collapsed variational inference. The result is a versatile tool that fits nicely into many differnt pipelines. For example, you can choose to make use of our quasi-mapping algorithm by providing Salmon with raw sequencing reads, or, if it is more convenient, you can provide Salmon with regular alignments (e.g. an unsorted BAM file produced with your favorite aligner), and it will use the same wicked-fast, state-of-the-art inference algorithm to estimate transcript-level abundances for your experiment.
Give salmon a try! You can find the latest binary releases here.
The current version number of the master branch of Salmon can be found here
NOTE: Salmon works by (quasi)-mapping sequencing reads directly to the transcriptome. This means the Salmon index should be built on a set of target transcripts, not on the genome of the underlying organism. If indexing appears to be taking a very long time, or using a tremendous amount of memory (which it should not), please ensure that you are not attempting to build an index on the genome of your organism!
The documentation for Salmon is available on ReadTheDocs, check it out here.
You can chat with the Salmon developers and other users via Gitter!
