Alternative splicing detection bioinformatics tools

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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.

Trinity

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.

Subread

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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.

MISO / Mixture of Isoforms

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.

ALEXA-Seq

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.

Tuxedo

Automatically manages the RNA-sequencing pipeline based on the TopHat, Cufflinks and CummeRbund suite of software. Tuxedo allows to assess alternative splicing (AS) inferred on fragments per kilobase per million (FPKM) values.

AStalavista / Alternative Splicing TrAscriptional LAndscape VISualization Tool And more

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.

KisSplice

Detects variants such as single nucleotide polymorphisms (SNPs), indels and alternative splicing (AS) in transcriptomes. KisSplice is a standalone software able to identify bubble patterns generated by AS events without the need of a reference genome. The application can be used to census AS events in various species, however it is suited only for splicing not for the reconstruction of an entire transcript.

IsoEM

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.

rMATS / replicate Multivariate Analysis of Transcript Splicing

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.

AltAnalyze

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).

outrigger

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.

SUPPA

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.

SpliceGrapher

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.

JuncBASE

It is used to identify and classify alternative splicing events from RNA-Seq data.

SplitSeek

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.

SQANTI / Structural and Quality Annotation of Novel Transcript Isoforms

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.

SAVnet / Splicing-Associated Variant detection by NETwork modeling

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).

DiffSplice

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.

OLego

Finds junction alignments using a multiple-seed and-extend approach. OLego is designed for fast de novo mapping of spliced mRNA-Seq reads with both high specificity and sensitivity. It aligns each read independently in one pass, without filtering of junctions based on their summary statistics derived from all reads. This application achieves both higher sensitivity and accuracy in discovery of exon junctions and micro-exons using realistic simulated data.

rDiff

Detects differential abundances of RNA isoforms in pairs of biological samples. rDiff is composed of two approaches: (i) rDiff.parametric supplies a method that can be used to identifying regions with alternative isoform expression; and (ii) rDiff.nonparametric, based on permutations, that does not depend of the underlying isoform structure and is especially suited for newly sequenced genomes only determined by homology.

SplicePie

A classification of RNA-Seq reads based on three major stages of splicing: pre-, intermediate- and post-splicing. SplicePie offers a number of approaches and solutions to study splicing in more details. The proposed strategy performs well on different sample preparations (sequencing the whole pool of RNAs or capturing a gene with different relative quantities of pre- and mature mRNA).

SigFuge

Tests significance of clustering in RNA-seq data. SigFuge allows to identify genomic loci exhibiting differential transcription patterns across many RNA-seq samples. It combines clustering with hypothesis testing to identify genes exhibiting alternative splicing, or differences in isoform expression. SigFuge is presented as a method capable of unsupervised discovery of differential isoform events in RNA-seq. This approach of studying gene expression as per-base expression curves along transcriptome coordinates makes it possible to identify differential events without strictly constraining the analysis to proposed exon or transcript boundaries.

MaxInfo

Allows identification and quantification of isoforms based on information coding theory. MaxInfo considers isoforms and reads as the ‘signal sources’ and ‘short codes’ of an information transmission channel, respectively. It tackles the isoform discovery problem from an information theory perspective. This tool is flexible and can be integrated with these advanced modifications for potential performance improvements.

SEASTAR / Systematic Evaluation of Alternative Transcription Start Sites in RNA

Permits identification of alternative first exons (FEs) and alternative tandem transcription start sites (TSSs) and quantification of their expression levels. SEASTAR utilizes a logistic regression method to identify FEs, including novel exons that are not present in the current transcriptome annotation. Furthermore, this tool can be applied to an RNA-seq dataset derived from the time course of reprogramming mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs).

DEGseq

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.

NGS-Trex / NGS TRanscriptome profile EXplorer

Allows user to upload raw sequences and obtain an accurate characterization of the transcriptome profile. NGS-Trex can assess differential expression at both gene and transcript level. It compares the expression profile of different samples. All comparisons are performed using a custom database which is mainly populated with several sources obtained from the NCBI. The tool allows user to discard ambiguously assigned reads or to assign those reads to all competing genes in the case of ambiguities.

casper

Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision. The goal is to provide recommendations tailored to each study, such as sequencing settings, the potential benefits of conducting further experimentation or the relative merits of different data analysis strategies.

SpliceTrap

Quantifies local exon inclusion levels in paired-end RNA-seq data. SpliceTrap is a method to generates alternative splicing profiles for different splicing patterns, such as exon skipping, alternative 5’ or 3’ splice sites, and intron retention. It relies on RNA-seq and can determine the inclusion level of every exon within a single cellular condition, without requiring a background set of reads.

SparseIso

Allows identification of isoforms from RNA-seq data. SparseIso is a Bayesian method that considers the reads falling on both splice junctions and exons. In this software, the transcript abundance is sampled considering all candidate isoforms to find a global view of isoform selection. The preference of selecting isoforms is determined by both the expression state and the correlation of isoform structure modeled in the covariance matrix. SparseIso allows the false transcripts to have reasonable low abundance.

SpliceSeq

A tool for investigating alternative mRNA splicing in next generation mRNA sequence data. SpliceSeq displays intuitive visualizations and prioritized lists of results that highlight splicing events and their biological consequences. SpliceSeq unambiguously aligns reads to gene splice graphs, facilitating accurate analysis of large, complex transcript variants that cannot be adequately represented in other formats.

IsoSeq_AS_de_novo

Characterizes and identifies bona fide alternatively spliced transcripts in any non-model system that lacks a reference genome sequence. IsoSeq_AS_de_novo can be applied to a non-model system with limited genetic resources. It returns a list of read alignments which represents AS event candidates. This platform provides better recovery on large transcripts and detects more Alternative Splicing (AS) events than can be recovered from transcriptome assemblies based on short reads.

SplAdder

An alternative splicing toolbox, that takes RNA-Seq alignments and an annotation file as input to i) augment the annotation based on RNA-Seq evidence, ii) identify alternative splicing events present in the augmented annotation graph, iii) quantify and confirm these events based on the RNA-Seq data, and iv) test for significant quantitative differences.

Sequgio

Assists users for joint estimation of isoform-level expression and isoform-specific read distribution. Sequgio is a method using RNA-Seq data from multiple samples to estimate the isoforms expression, taking into account non-uniform read distribution. This approach provides substantial improvement on the quality of model fitting and improves the sensitivity in isoform-level differential expression analysis.

Sircah

An application written in python that detects and visualizes alternative splicing events using spliced alignments. Sircah takes as input transcript models in the GFF3 format allowing the user the flexibility to choose the sources of evidence for the use in detecting alternative transcription.

SNPlice

A computational approach for identifying cis-acting, splice-modulating variants from RNA-seq datasets. SNPlice mines RNA-seq datasets to find reads that span single nucleotide variant (SNV) loci and nearby splice junctions, assessing the co-occurrence of variants and molecules that remain unspliced at nearby exon-intron boundaries. Hence, SNPlice highlights variants preferentially occurring on intron-containing molecules, possibly resulting from altered splicing.

PSGInfer

Analyzes RNA-Seq data with probabilistic splice graph (PSG) models of gene alternative processing. PSGInfer is able to: (1) construct PSG models from known transcript annotations, (2) estimate maximum likelihood (ML) or maximum a posteriori (MAP) of PSG parameters given an RNA-Seq data set, and (3) predict genes that are differentially processed (DP) between two samples, given RNA-Seq data for each sample.

aRNApipe / automated RNA-seq pipeline

Analyzes single-end and stranded or unstranded paired-end RNA-seq data. aRNApipe focuses on high performance computing (HPC) environments and the independent designation of computational resources at each stage allowing optimization of HPC resources. It is highly flexible because its project configuration and management options. This tool can be adapted to changes in the current applications and the addition of new functionalities. It allows users to complete primary RNA-seq analysis.

rSeqNP

Implements a non-parametric approach to test for differential expression and splicing from RNA-Seq data. rSeqNP uses permutation tests to access statistical significance and can be applied to a variety of experimental designs. By combining information across isoforms, rSeqNP is able to detect more differentially expressed or spliced genes from RNA-Seq data.

TSIS / Time-Series Isoform Switch

Detects and characterizes temporal and complex isoform switches. TSIS recognizes pairs of alternative splicing (AS) transcripts with one or more isoform switches and genes with multiple pairs of transcripts which show isoform switches. It is based on score schemes from current methods and incorporates metrics which capture the characteristics of the isoform switches. This tool provides histograms that show the number of switches happening at each time-point.

SDEAP

A differential transcript expression (DTE) analysis algorithm. SDEAP estimates the number of conditions directly from the input samples using a Dirichlet mixture model and discovers alternative splicing events using a new graph modular decomposition algorithm. By taking advantage of the above technical improvement, SDEAP was able to outperform the other DTE analysis methods in extensive experiments on simulated data and real data with qPCR validation. The prediction of SDEAP also allows users to classify the samples of cancer subtypes and cell-cycle phases more accurately.

MAJIQ / Modeling Alternative Junction Inclusion Quantification

Provides a method to detect, quantify and visualize differential splicing between groups of experiments. Two key features distinguish MAJIQ from other algorithms. First, MAJIQ does not quantify whole gene isoforms. Instead, MAJIQ defines a more general concept of “local splicing variations”, or LSVs. Briefly, LSVs are defined as splits in a gene splice graph where a reference exon is spliced together with other segments downstream (single source LSV) or upstream of it (single target LSV). The second important distinguishing element of MAJIQ is that it allows users to supplement previous transcriptome annotation with reliably-detected de-novo junctions from RNA-Seq experiments.

PathwaySplice

Performs pathway analysis of alternative splicing in RNA-Seq data. PathwaySplice consists of five mains features : (i) a fitted analysis according the number of exons associated with each gene; (ii) a selection bias visualization; (iii) a use of logistic regression to evaluate the presence of bias; (iv) a determination of the significant genes involved in pathway significance; and (v) the generation of an enrichment map made of significant pathways. It can be used with various datasets including user-defined ones.

Equivalent Junctions

New

Assists users in extracting equivalent junctions for a genome. Equivalent Junctions is a python package that contains scripts to generate an equivalent junction sequence per junction for each exon-exon junction. A command also provides the total number of each equivalent junction sequence. The supplied codes are general and can be used for any genome.

ChopStitch

Retrieves putative exons and builds splice graphs. ChopStitch employs an assembled transcriptome and whole genome shotgun sequencing (WGSS) data to proceed. Using a Bloom filter, it can recognize exon-exon boundaries in de novo assembled RNA-seq data. This tool is able to identify base substitutions in transcript sequences corresponding to sequencing or assembly errors, haplotype variations, or putative RNA editing events.

IDP-denovo

Aims to characterize non-model organisms. IDP-denovo allows users to handle transcriptome data without a reference genome. It offers a platform that consists of three main features: (i) it assembles hybrid sequencing data; (ii) it annotates gene isoform structures and alternative splice sites and; (iii) it quantifies isoform abundance by using both short (SRs) and long reads (LRs). The software is suited to be incorporated into automated pipelines.

EBChangePoint / Empirical Bayes Change-Point model

Allows recognition of alternative 3' splice sites (SS) and 5' SS. EB Chang Point does not rely on annotation information. It provides a systematic framework permitting integration of various information when available. This tool pools information across genes to improve detection efficiency. It offers a way for users to choose to address different levels of questions, namely, whether alternative 3' SS or 5' SS happens, and/or where it happens.

Mikado

Provides an approach for integrating transcript assemblies. Mikado is a pipeline that prepares, serializes and picks annotations files to allow users to obtain a set of gene models. these models are filtered according to individual requirements by using different algorithms for defining loci, scoring transcripts, to ultimately determine a representative transcript for each locus. This software aims to improve precision over the original assemblies, with minimal drops in recall.

SL-quant

Numbers short spliced leader (SL) trans-splicing events from RNAseq data. SL-quant provides a pipeline which considers unmapped reads starting from the hypothesis that reads including SL are those which don’t map with the genome or transcriptome chosen as reference. This program can be used for determining 3’ trans-splice sites, at single-nucleotide resolution, as well as for censusing SL trans-splicing events, at a gene level.

RACKJ / Read Analysis & Comparison Kit in Java

Provides a collection of software to investigate and compare RNA-seq data obtained by next generation sequencing (NGS) technologies. RACKJ can calculate the number of reads matching to exons and introns, mapping splice junctions (SJs) according to the alignment of reads to the genome. It allows the comparison of two samples and the recognition of genes with most significant difference in exon (splicing)-level.

Alternative splicing identification software tools | RNA sequencing data analysis