Alternative splicing identification software tools | RNA sequencing data analysis
Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis.
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.
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.
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.
Assists in profiling and comparing alternative splicing events in RNA-Seq data. VAST-TOOLS is an application developed for evolutionary comparisons. It works synergistically with the VastDB web server and with Matt, a toolkit for downstream analyses of alternative splicing. This method contains several main sub-commands, such as 'align', 'combine', 'merge', 'tidy', 'compare', 'diff' and 'plot'.
Offers a model for alternative splicing (AS) at exon or isoform level. MISO is a program that uses information in single-end or paired-end RNA-seq data and a Bayesian inference to estimate the probability for a read to be issued from a particular isoform. The program is available through two packages: in C language (fastmiso) or in Python language (misopy). The application supplies confidence intervals (CIs) for: (i) estimating of exon and isoform abundance, (ii) identifying differential expression. It can be applied for analyzing isoform regulation.
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.
Analyzes parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. ALEXA-Seq comprises several functions: (1) creation of a database of expression and alternative expression sequence ‘features’, (2) mapping of short paired-end sequence reads to these features, (3) identification of features that are expressed above background noise while taking into account locus-by-locus noise, or (4) identification of features that are differentially expressed in samples.
Allows identification, extraction and displaying of complex alternative splicing (AS) events from annotated genes. AStalavista is an alternative splicing transcriptional landscape visualization tool for investigating and comparing types and distributions of the different AS events found in whole genome annotations and user provided gene sets. The software enables identification of arbitrarily complex combinations of hitherto described AS events, either visually or by representation in a univocal notation system. It can be used if the sequencing/annotation process has not been completed.
Allows expression level estimation and differential expression (DE) from RNA-Seq data. IsoEM uses bootstrapping to infer confidence intervals for gene and isoform expression level estimates. The differential expression tool IsoDE, included in the package, performs DE analysis using bootstrap samples generated by IsoEM2. The main feature of these tools is the fast non-parametric computation of confidence intervals and identification of DE genes based on bootstrapping.
A statistical model and computer program designed for detection of differential alternative splicing from replicate RNA-Seq data. rMATS uses a hierarchical model to simultaneously account for sampling uncertainty in individual replicates and variability among replicates. In addition to the analysis of unpaired replicates, rMATS also includes a model specifically designed for paired replicates between sample groups. The hypothesis-testing framework of rMATS is flexible and can assess the statistical significance over any user-defined magnitude of splicing change. The old version of rMATS was called MATS.
An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichment and more).
Uses junction reads from RNA seq data, and a graph database to create a de novo alternative splicing annotation with a graph database. Outrigger is a Python package and an RNA-seq analysis software that quantify percent spliced-in (Psi) of the events. It finds novel splicing events, including novel exons and was developed to help user to be confident in alternative exon inclusion calculations. It is recommended to use the Anaconda Python Distribution and creates an environment to install outrigger.
Allows to analyze differential splicing. SUPPA measures differential splicing between conditions by exploiting the variability between biological replicates to determine the uncertainty in the proportion spliced-in (PSI) values. The software is also able to analyze multiple conditions by computing the pairwise differential splicing between conditions, and can detect groups of events with similar splicing patterns across conditions using density-based clustering.
Detects, quantifies and displays differential splicing between groups of experiments. MAJIQ defines a general concept of local splicing variations (LSVs). It enables users to add previous transcriptome annotation with reliably-detected de-novo junctions from RNA-Seq experiments. This tool can capture all types of alternative splicing (AS) and many other variations which are more complex.
Predicts splice graphs from RNA-Seq and expressed sequence tag (EST) data in order to enhance existing gene annotations. SpliceGrapher includes modules for recognizing alternative splicing (AS) events and for viewing predicted splice graphs along with the evidence employed to construct them. It can make predictions for genes that have low read coverage. This tool assists users to resolve AS events that are otherwise hard to detect from short-read data.
Identifies splice junctions. SplitSeek allows de novo prediction of splice junctions in short-read RNA-seq data. The software consists of two programs that are executed sequentially. It can detect novel splice events and be used as a way to extend known gene models. The results can be directly uploaded to the UCSC genome browser and used as input to the BEDTools software suite, which enables user to visualize and analyze the predicted events in a genomic context.
Provides a wide range of descriptors of transcript quality and generates a graphical report to aid in the interpretation of the sequencing results. SQANTI is a pipeline for the in-depth characterization of isoforms obtained by full-length transcript sequencing, which are commonly returned in a fasta file format without any extra information about gene/transcript annotation or attribute description. This software is oriented to be used for characterization of isoforms generated by PacBio Iso-Seq pipeline. Besides, it can be applied to any organism.
Identifies splicing-associated variants (SAVs). SAVnet is an approach for detecting SAVs based on a list of somatic variants in a cohort and its matched RNA sequencing (RNA-seq) data using a rigorous statistical framework. It was used to perform a comprehensive analysis of a large number of primary cancer samples across 31 cancer types from The Cancer Genome Atlas (TCGA).
Detects and visualizes of differential alternative transcription. DiffSplice is an ab initio method to detect alternative splicing isoforms that are differentially expressed under different conditions using high-throughput RNA-seq reads. This software directly localizes where differential splicing occurs, making it easier to identify exons involved in alternative transcription. It estimates the relative proportion of alternative transcription flows in every ASM and calculates the Jensen–Shannon divergence (JSD) to quantify the difference in transcription between samples.