TopHat : A fast splice junction mapper for RNA-Seq reads.
QPALMA : A tool for Optimal Spliced Alignments of Short Sequence Reads .
MapSplice : A tool for accurate mapping of RNA-seq reads for splice junction discovery .
SpliceMap : A de novo splice junction discovery and alignment tool.
GMAP : A genomic mapping and alignment program for mRNA and EST sequences .
STAR : (Spliced Transcripts Alignment to a Reference) Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
SOAPsplice : A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.
Supersplat : An application for discovering potential splice junctions in high throughput sequencing (HTS) data.
CuffDiff :assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
EdgeR : (Empirical analysis of digital gene expression data in R) tool for Differential expression analysis of RNA-seq and digital gene expression profiles with biological replication.
DESeq :An R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression.
Myrna : cloud computing tool for calculating differential gene expression in large RNA-seq datasets.
CuffDiff :assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
MISO : (Mixture of Isoforms) A probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.
DEXseq : Package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs.
Alexa-seq : Method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.
SOAPdenovo-Trans : A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.
defuse: A software package for discovering gene fusion from RNA-Seq data.
FusionAnalyser: A software to read paired reads mapping to different genes (Bridge reads), generated through high-throughput whole transcriptome sequencing.
FusionHunter: A tool to identify fusion transcripts from transcriptional analysis of paired-end RNA-seq.
FusionMap: An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions.
FusionSeq: A tool to identify fusion transcripts from paired-end RNA-sequencing.
SOAPfusion : A novel tool for fusion discovery with paired-end RNA-Seq reads .
TopHat-Fusion : Enhanced version of TopHat with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. .