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De novo transcriptome assembly software tools | RNA sequencing data analysis

De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance,…
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SPAdes
Desktop

SPAdes

A single-cell assembler for capturing and sequencing “microbial dark…

A single-cell assembler for capturing and sequencing “microbial dark matter” that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes…

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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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EBARDenovo
Desktop

EBARDenovo Extension, Bridging And Repeat-sensing Denovo

Assembles paired-end RNA-Seq data. EBARDenovo is based on a bi-directional…

Assembles paired-end RNA-Seq data. EBARDenovo is based on a bi-directional expansion method using paired-end RNA-Seq data to guide the transcriptome assembly. The software is suited for detecting…

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Trans-ABySS
Desktop

Trans-ABySS

Allows users to analyze ABySS-assembled contigs from shotgun transcriptome…

Allows users to analyze ABySS-assembled contigs from shotgun transcriptome data. Trans-ABySS is a standalone software composed of two modules: transabyss that performs assembling of RNAseq data and…

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MIRA
Desktop

MIRA Mimicking Intelligent Read Assembly

Uses a Swiss army knife of sequence assembly developed and used in the past 16…

Uses a Swiss army knife of sequence assembly developed and used in the past 16 years to get assembly jobs done efficiently - and especially accurately. MIRA is a whole genome shotgun (WGS) and EST…

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STM
Desktop

STM Scaffolding using Translation Mapping

Allows de-novo assembly of transcriptome using a reference proteome. STM…

Allows de-novo assembly of transcriptome using a reference proteome. STM exploits the fact that, by translating contigs into amino acid sequences, it is possible to search for orthologous regions in…

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Oases
Desktop

Oases

A de novo transcriptome assembler designed to produce transcripts from short…

A de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.

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SOAPdenovo-Tran…
Desktop

SOAPdenovo-Trans

A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to…

A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.

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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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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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SparseIso
Desktop

SparseIso

Allows identification of isoforms from RNA-seq data. SparseIso is a Bayesian…

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…

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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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Rnnotator
Desktop

Rnnotator

Assembles Illumina single or paired-end reads and incorporates strand-specific…

Assembles Illumina single or paired-end reads and incorporates strand-specific RNA-Seq reads into the assembly. Rnnotator is an automated software pipeline that consists of three major components:…

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Bridger
Desktop

Bridger

A de novo transcriptome assembler that takes advantage of techniques employed…

A de novo transcriptome assembler that takes advantage of techniques employed in Cufflinks to overcome limitations of the existing de novo assemblers. When tested on dog, human and mouse RNA-seq…

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IDBA-Tran
Desktop

IDBA-Tran

Assembles reads to reconstruct expressed transcripts. IDBA-Tran calculates the…

Assembles reads to reconstruct expressed transcripts. IDBA-Tran calculates the probability that a k-mer or short simple path contains error by using both their multiplicity and a multi-normal…

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ASplice
Desktop

ASplice

Recovers alternatively spliced isoforms and expression levels. ASplice…

Recovers alternatively spliced isoforms and expression levels. ASplice constructs splicing graphs for RNA-Seq libraries. It enumerates k-mer frequencies in the first stage to reduce memory…

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SATRAP
Desktop

SATRAP SOLiD Assembler TRAnslation Program

A computer program designed to efficiently translate de novo assembled…

A computer program designed to efficiently translate de novo assembled color-space sequences into a base-space format. The program was tested and validated using simulated and real transcriptomic…

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Glutton
Desktop

Glutton

Differentiates paralogous genes for RNA-seq data from non-model organisms.…

Differentiates paralogous genes for RNA-seq data from non-model organisms. Glutton connects discontiguous sequences by scaffolding contigs where there is either insufficient overlap or coverage for…

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Shannon
Desktop

Shannon

Consistes in a RNA-Seq assembler. Shannon can determine the transcriptome and…

Consistes in a RNA-Seq assembler. Shannon can determine the transcriptome and can exploit the fact that the abundance in the incoming and outgoing edge are the same. This tool is useful for…

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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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DRAP
Desktop

DRAP De novo RNA-seq Assembly Pipeline

Wraps two assemblers (Trinity and Oases) in order to improve their results…

Wraps two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP is a de novo RNA-Seq Assembly Pipeline that reduces from 1.3 to 15 fold the…

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BinPacker
Desktop

BinPacker

A de novo algorithm to assemble full-length transcripts by remodeling the…

A de novo algorithm to assemble full-length transcripts by remodeling the problem as tracking a set of trajectories of items over a splicing graph. This approach, which subtly integrates the coverage…

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KisSplice
Desktop

KisSplice

A piece of software that enables the analysis of RNA-seq data with or without a…

A piece of software that enables the analysis of RNA-seq data with or without a reference genome.

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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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FRAMA
Desktop

FRAMA from RNA-seq to annotated mRNA assembly

A genome-independent annotation tool for de novo mRNA assemblies that addresses…

A genome-independent annotation tool for de novo mRNA assemblies that addresses several post-assembly tasks, such as reduction of contig redundancy, ortholog assignment, correction of misassembled…

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Mikado
Desktop

Mikado

Provides an approach for integrate transcript assemblies. Mikado is a pipeline…

Provides an approach for integrate transcript assemblies. Mikado is a pipeline that prepares, serializes and picks annotations files for allowing users to obtain a set of gene models filtered…

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TraRECo
Desktop

TraRECo

Allows users to build splicing graph in linear time of data size. TraRECo…

Allows users to build splicing graph in linear time of data size. TraRECo provides a reliable splicing graph construction, which is useful to explore not-yet-discovered isoforms and must be able to…

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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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annotatingTrans…
Desktop

annotatingTranscriptomes

Allows users to annotate de novo transcriptomes. annotatingTranscriptomes is a…

Allows users to annotate de novo transcriptomes. annotatingTranscriptomes is a custom Perl script allowing to annotate with gene names, Gene Ontology (GO) terms, EuKaryotic Orthologous Groups (KOG)…

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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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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…

CAP3
Web

CAP3

The third generation of the CAP sequence assembly program. The CAP3 program…

The third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 58 and 38 low-quality regions of…

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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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EasyCluster
Desktop

EasyCluster

Performs an effective detection of splicing isoforms, since it can refine…

Performs an effective detection of splicing isoforms, since it can refine exon-exon junctions and explore alternative splicing without known reference transcripts. Results in GFF3 format can be…

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ViennaNGS
Desktop

ViennaNGS

An integrated collection of Perl modules focused on building efficient…

An integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. ViennaNGS comes with functionality for extracting and converting features from common NGS…

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Newbler
Desktop

Newbler GS De novo assembler

A software package for de novo DNA sequence assembly.

A software package for de novo DNA sequence assembly.

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BRANCH
Desktop

BRANCH

A software tool that extends de novo transfrags and identifies novel transfrags…

A software tool that extends de novo transfrags and identifies novel transfrags with DNA contigs or genes of close related species. BRANCH discovers novel exons first and then extends/joins…

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TransPS
Desktop

TransPS

A pipeline for post-processing of pre-assembled transcriptomes using reference…

A pipeline for post-processing of pre-assembled transcriptomes using reference based method. TransPS applies an align-layout-consensus structure, consisting of three major stages. First, query…

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optimize…
Desktop

optimize assembler

Optimizes de novo assembly of short-read RNA-seq data for phylogenomics.…

Optimizes de novo assembly of short-read RNA-seq data for phylogenomics. optimize_assembler is a package that contains scripts to extract nuclear reads with Oases, Trinity, Trans-ABySS,…

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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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SSP
Desktop

SSP

A de novo transcriptome assembler that assembles RNA-seq reads into…

A de novo transcriptome assembler that assembles RNA-seq reads into transcripts. SSP aims to reconstructs all the alternatively spliced isoforms and estimates the expression level of them.…

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T-IDBA
Desktop

T-IDBA Iterative De Bruijn graph de novo Assembler for transcriptome

Offers a de novo short read assembler dedicated to transcriptome. T-IDBA…

Offers a de novo short read assembler dedicated to transcriptome. T-IDBA divides a de Bruijn graph into many connected components, most of which represent isoforms from a single gene. It can generate…

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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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