Alternative splicing identification software tools | RNA sequencing data analysis

Builds transcriptomes from RNA-seq data. Trinity is a standalone software composed of three main components: (i) Inchworm, that first generates transcript contigs; (ii) Chrysalis, for clustering them and constructing complete de Bruijn graphs for each cluster and; (iii) Butterfly that processes individual graphs in parallel for finally resulting to the reconstruction of the transcript sequences.

Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks assembles individual transcripts from RNA-seq reads that have been aligned to the genome. This software is able to infer the splicing structure of each gene because reads from multiple splice variants for a given gene can be found in a sample. Quantification of transcript abundances is also possible by preferring a reference annotation to assembling the reads.

Assists users in mapping reads to a reference genome. Subread offers a suite of programs for processing next-generation sequencing read data. This package includes Subread (an aligner), Subjunc (an aligner), Sublong (a long-read aligner), Subindel (a long indel detection program), featureCounts (a read quantification program), exactSNP (an SNP calling program) and other utility programs.

Identifies differentially expressed genes or isoforms for RNA-seq data from different samples. DEGseq encourages users to export gene expression values in a table format which could be directly processed by edgeR. It is based on the random sampling model which fits well the random sampling model. This tool can be applied to recognize differential expression of exons or pieces of transcripts.

Allows users to handle RNA-sequencing pipeline based on the TopHat, Cufflinks and CummeRbund suite of software. Tuxedo is a program that enables assessment of alternative splicing (AS) inferred on fragments per kilobase per million (FPKM) values. It can assist researchers to detect genes and splicing variants and compare gene expression and transcripts under different conditions.