StringTie assembles aligned RNA-Seq reads into transcripts that represent splice variants in RNA-Seq samples.
Cufflinks is a program that analyzes RNA -Seq samples. It assembles aligned RNA-Seq reads into a set of transcripts, then inspects the transcripts to estimate abundances and test for differential expression and regulation in the RNA-Seq reads.
HISAT2 is a graph-based alignment program that maps DNA and RNA sequencing reads to a population of human genomes.
TopHat uses Bowtie, a high-throughput short read aligner, to analyze the mapping results for RNA-Seq reads and identify splice junctions.
Please note that tophat (and bowtie) cannot run in parallel, that is, on multiple nodes. Submitting multi-node jobs will only waste resources. In addition you must explicitly include the '-p' option to use multiple threads on a single node.
TAU Commander is a user interface for the TAU Performance System, a set of tools for analyizing the performance of parallel programs.
Salmon is a tool for quantifying the expression of transcripts using RNA-seq data.
Kallisto is an RNA-seq quantification program. It quantifies abundances of transcripts from RNA-seq data and uses psedoalignment to determine the compatibility of reads with targets, without needing alignment.