Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It requires a set of target transcripts (either from a reference or de-novo assembly) to quantify. All you need to run Salmon is a FASTA file containing your reference transcripts and a (set of) FASTA/FASTQ file(s) containing your reads. Optionally, Salmon can make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads.
Salmon is open source software under the GNU General Public License v3.0