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Genome-guided transcriptome assembly software tools | RNA sequencing data analysis

A reference-based or genome-guided transcriptome assembly algorithm uses alignments of reads to the genome that are produced by a specialized spliced-alignment tool, such as TopHat2 (Kim et al., 2013) or GSNAP (Wu and Nacu, 2010), to identify…
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Cufflinks
Desktop

Cufflinks

Assembles transcripts, estimates their abundances, and tests for differential…

Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.

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Trinity
Desktop

Trinity

A method for the efficient and robust de novo reconstruction of transcriptomes…

A method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

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RSEM
Desktop

RSEM RNA-Seq by Expectation-Maximization

An user-friendly software package for quantifying gene and isoform abundances…

An user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data.

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Scripture
Desktop

Scripture

A method for transcriptome reconstruction that relies solely on RNA-Seq reads…

A method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage…

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StringTie
Desktop

StringTie

A fast and highly efficient assembler of RNA-Seq alignments into potential…

A fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de…

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G-Mo.R-Se
Desktop

G-Mo.R-Se Gene MOdeling using RNA-Seq

A method aimed at using RNA-Seq short reads to build de novo gene models.…

A method aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio…

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Chipster
Desktop

Chipster

A user-friendly analysis software tool for high-throughput data. Chipster…

A user-friendly analysis software tool for high-throughput data. Chipster contains over 350 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can…

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iReckon
Desktop

iReckon

An algorithm for the simultaneous isoform reconstruction and abundance…

An algorithm for the simultaneous isoform reconstruction and abundance estimation.

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SpliceGrapher
Desktop

SpliceGrapher

Predicts alternative splicing patterns and produces splice graphs that capture…

Predicts alternative splicing patterns and produces splice graphs that capture in a single structure the ways a gene's exons may be assembled. SpliceGrapher enhances gene models using evidence…

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TransComb
Desktop

TransComb

A genome-guided transcriptome assembler for RNA-seq data. TransComb can…

A genome-guided transcriptome assembler for RNA-seq data. TransComb can assemble all transcripts from short paired-end reads using a reference genome and analyze their abundances. It was developed…

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CIDANE
Desktop

CIDANE Comprehensive Isoform Discovery and AbuNdance Estimation

A framework for genome-based transcript reconstruction and quantification.…

A framework for genome-based transcript reconstruction and quantification. CIDANE is engineered to not only assembly RNA-seq reads ab initio, but to also make use of the growing annotation of known…

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Bayesembler
Desktop

Bayesembler

A probabilistic method for transcriptome assembly built on a Bayesian model of…

A probabilistic method for transcriptome assembly built on a Bayesian model of the RNA sequencing process. Under this model, samples from the posterior distribution over transcripts and their…

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UnoSeq
Desktop

UnoSeq

A Java library to analyze next generation sequencing data and especially…

A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists.

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Rockhopper
Desktop

Rockhopper

A comprehensive and user-friendly system for computational analysis of…

A comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ,…

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FlipFlop
Desktop

FlipFlop

Implements a fast method for de novo transcript discovery and abundance…

Implements a fast method for de novo transcript discovery and abundance estimation from RNA-seq data. FlipFlop differs from Cufflinks by simultaneously performing the identification and quantitation…

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CAFE
Desktop

CAFE Co-Assembly of stranded and unstranded RNA-seq data Followed by End-correction

Improves the original assemblies, respectively assembled with stranded and/or…

Improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data. CAFE is a high-performing transcriptome assembly pipeline that enables to predict the directions…

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Traph
Desktop

Traph Transcrips in gRAPHs

Allows to identify and quantify transcript. Traph is a de novo genome-based…

Allows to identify and quantify transcript. Traph is a de novo genome-based tool with two-fold advantage: (i) it translates a problem as an established one in the field of network flows, which can be…

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CEM
Desktop

CEM

An algorithm to assemble transcripts and estimate their expression levels from…

An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

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MiTie
Desktop

MiTie Mixed Integer Transcript IdEntification

Offers a framework for transcriptome reconstruction. MiTie starts from a…

Offers a framework for transcriptome reconstruction. MiTie starts from a selection of a set of transcripts for determining and quantifying RNA-Seq-based transcript simultaneously in several samples.…

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Oqtans
Desktop

Oqtans Online quantitative transcriptome analysis

It is based on the Galaxy-framework and provides tools for read mapping,…

It is based on the Galaxy-framework and provides tools for read mapping, transcript reconstruction and quantitation as well as differential expression analysis.

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IsoLasso
Desktop

IsoLasso

An algorithm used to assemble transcripts and estimate their expression levels…

An algorithm used to assemble transcripts and estimate their expression levels from RNA-Seq reads. Three mains goals are reached by IsoLasso: the maximization of prediction accuracy, minimization of…

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RNA-seq portal
Web

RNA-seq portal

Includes three types of workflows for different tasks. RNA-seq portal permits…

Includes three types of workflows for different tasks. RNA-seq portal permits users to perform computing and analysis, including sequence quality control, read-mapping, transcriptome assembly,…

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NMFP
Desktop

NMFP Non-negative Matrix Factorization Preselection

A preselection method which is designed to improve the accuracy of…

A preselection method which is designed to improve the accuracy of computational methods in identifying mRNA isoforms from RNA-seq data. Through simulation and real data studies, NMFP can effectively…

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SLIDE
Desktop

SLIDE

We have developed a statistical method that takes exon boundaries and RNA-Seq…

We have developed a statistical method that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample.

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necklace
Desktop

necklace

Automatically combines transcriptomes from difference sources, such as assembly…

Automatically combines transcriptomes from difference sources, such as assembly and annotation, into a compact and unified reference. necklace is applicable to any species with an incomplete…

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RNA workbench
Server

RNA workbench

Establishes a central, redistributable workbench for scientists and programmers…

Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in…

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RNA-Rocket
Web

RNA-Rocket

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for…

A free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations, and the…

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SAMMate
Desktop

SAMMate

An open source GUI software suite to process RNA-Seq data. It is composed of…

An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate. assemblySAM employs a novel method to localize and assemble RNA-seq reads into RNA…

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TCW
Desktop

TCW Transcriptome Computational Workbench

A software package for assembling, annotating, querying, and comparing…

A software package for assembling, annotating, querying, and comparing transcript and expression level data.

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QuickNGS
Desktop
Web

QuickNGS

A workflow system for laboratories with the need to analyze data from multiple…

A workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and…

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Voskhod
Desktop

Voskhod

A direct read to genome mapping pipeline that recovers 94.8% of the genes…

A direct read to genome mapping pipeline that recovers 94.8% of the genes irrespective of read length at 0% divergence. Voskhod allows conducting the transcriptome inference and gene expression…

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Strawberry
Desktop

Strawberry

Serves for transcript reconstruction and quantification from paired-end RNA-seq…

Serves for transcript reconstruction and quantification from paired-end RNA-seq data. Strawberry simplifies discovery of novel isoforms and calculation of transcript-level expression. It can process…

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ORA
Desktop

ORA Overlapped Reads Assembler

Allows a simple and reliable analysis of the transcriptome structure in…

Allows a simple and reliable analysis of the transcriptome structure in organisms with a low number of introns. ORA can also determine the size and the position of the untranslated regions (UTR) and…

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Astroid
Desktop

Astroid

An algorithm that simultaneously reconstruct transcripts and estimate their…

An algorithm that simultaneously reconstruct transcripts and estimate their abundance. The program takes read alignment as input in SAM format, and provides reconstructed transcripts in the standard…

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DRUT
Desktop

DRUT

Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated…

Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data.

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RCDA
Desktop

RCDA

A genome-based transcript assembly tool comprising RCluster, that recursively…

A genome-based transcript assembly tool comprising RCluster, that recursively clusters transcripts, and DAssemble, that generates composite transcript sequences through path-finding using a directed…

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Tuxedo
Desktop

Tuxedo

Handles RNA-sequencing pipeline that is based on TopHat suite. The Tuxedo…

Handles RNA-sequencing pipeline that is based on TopHat suite. The Tuxedo protocol allows to assess alternative splicing inferred on fragments per kilobase per million (FPKM) values.

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IsoInfer
Desktop

IsoInfer

Infers isoforms from short RNA-Seq reads and information concerning exon-intron…

Infers isoforms from short RNA-Seq reads and information concerning exon-intron boundaries and transcription start site (TSS) - poly-A site (PAS) pairs. IsoInfer can calculate the expression levels…

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CLIIQ
Desktop

CLIIQ

An algorithm to simultaneously identify and quantify expressed isoforms based…

An algorithm to simultaneously identify and quantify expressed isoforms based on RNA-Seq data from multiple sample(s) in a population.

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bcbio-nextgen
Desktop

bcbio-nextgen

A python toolkit providing best-practice pipelines for fully automated high…

A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters.…

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TAP
Web

TAP Transcript Assembly Program

Assembles the joint gene structure of the entire genomic region from individual…

Assembles the joint gene structure of the entire genomic region from individual splice junction pairs. TAP is a software tool developed to delineate gene structures using genomically aligned…

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MaLTA
Desktop

MaLTA

A method for simultaneous transcriptome assembly and quantification from Ion…

A method for simultaneous transcriptome assembly and quantification from Ion Torrent RNA-Seq data. This approach explores transcriptome structure and incorporates a maximum likelihood model into the…

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