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Spliced read alignment software tools | RNA sequencing data analysis

Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The…
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STAR
Desktop

STAR Spliced Transcripts Alignment to a Reference

Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.…

Aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. STAR has a potential for accurately aligning long (several kilobases) reads that are emerging from the third-generation…

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TopHat
Desktop

TopHat

Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput…

Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie. TopHat also analyzes the mapping results to identify splice junctions between exons. It can…

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GEM mapper
Desktop

GEM mapper GEnome Multitool mapper

Supplies a set of applications for indexing or querying sequence data. GEM is…

Supplies a set of applications for indexing or querying sequence data. GEM is composed of six modulable parts including: (i) core libraries; (ii) header files; (ii) standalones executables that…

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MapSplice
Desktop

MapSplice

A splice detection algorithm whose focus is high sensitivity and specificity in…

A splice detection algorithm whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice performs a sensitive, complete and unbiased…

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CIRCexplorer
Desktop

CIRCexplorer

A combined strategy to identify junction reads from back spliced exons and…

A combined strategy to identify junction reads from back spliced exons and intron lariats. CIRCexplorer is now only a circular RNA annotating tool, and it parses fusion junction information from…

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HISAT
Desktop

HISAT Hierarchical Indexing for Spliced Alignment of Transcripts

A fast and sensitive spliced alignment program for mapping RNA-seq reads. In…

A fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that…

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SpliceMap
Desktop

SpliceMap

Detects splice junctions from RNA-seq data. SpliceMap does not depend on any…

Detects splice junctions from RNA-seq data. SpliceMap does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and…

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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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Subread
Desktop

Subread

A toolkit for processing next-gen sequencing data. These programs were also…

A toolkit for processing next-gen sequencing data. These programs were also implemented in Bioconductor R package Rsubread.

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GSNAP
Desktop

GSNAP

Aligns both single- and paired-end reads as short as 14 nt and of arbitrarily…

Aligns both single- and paired-end reads as short as 14 nt and of arbitrarily long length. GSNAP can detect short- and long-distance splicing, including interchromosomal splicing, in individual…

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aRNApipe
Desktop

aRNApipe automated RNA-seq pipeline

Provides an integrated and efficient workflow for analyzing single-end and…

Provides an integrated and efficient workflow for analyzing single-end and stranded or unstranded paired-end RNA-seq data. Unlike previous pipelines, aRNApipe is focused on high performance computing…

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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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SPALN
Web
Desktop

SPALN

Allows users to map and align cDNA or protein sequences onto a whole genomic…

Allows users to map and align cDNA or protein sequences onto a whole genomic sequence (WGS). Spaln intends to improve automatic classification of alternative splicing and transcriptional initiation…

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RASER
Desktop

RASER Reads Aligner for SNPs and Editing sites of RNA

An accurate read aligner with novel mapping schemes and index tree structure…

An accurate read aligner with novel mapping schemes and index tree structure that aims to reduce false positive mappings due to existence of highly similar regions. RASER shows the best mapping…

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SplitSeek
Desktop

SplitSeek

Identifies splice junctions. SplitSeek allows de novo prediction of splice…

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…

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NGS-Trex
Web

NGS-Trex NGS TRanscriptome profile EXplorer

Allows user to upload raw sequences and obtain an accurate characterization of…

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…

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QuickRNASeq
Desktop

QuickRNASeq

Advances the automation and visualization of RNA-seq data analyses results.…

Advances the automation and visualization of RNA-seq data analyses results. QuickRNASeq is a pipeline that significantly reduces data analysts’ hands-on time, which results in a substantial…

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RUM
Desktop

RUM

An alignment, junction calling, and feature quantification pipeline…

An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data.

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CRAC
Desktop
Web

CRAC Complex Reads Analysis & Classification

An RNA-Seq mapping software tool that include the discovery of transcriptomic…

An RNA-Seq mapping software tool that include the discovery of transcriptomic and genomic variants like splice junction, chimeric junction, SNVs, Indels in a single analysis step using a built-in…

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OLego
Desktop

OLego

A program specifically designed for de novo spliced mapping of mRNA-seq reads.…

A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper.

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PRADA
Desktop

PRADA

A pipeline to analyze paired end RNA-Seq data to generate gene expression…

A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.

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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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TrueSight
Desktop

TrueSight

Allows splice junction (SJ) detection. TrueSight is a method developed to…

Allows splice junction (SJ) detection. TrueSight is a method developed to improve sensitivity and specificity of mapping SJ spanning RNA-seq reads. The software incorporates information from (i)…

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QPALMA
Desktop

QPALMA

An alignment tool targeted to align spliced reads produced by Next Generation…

An alignment tool targeted to align spliced reads produced by Next Generation sequencing platforms such as Illumina Solexa or 454.

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FANSe2splice
Desktop

FANSe2splice

Provides very low false positive rates (FDR) in detecting splice junctions.…

Provides very low false positive rates (FDR) in detecting splice junctions. FANSe2splice is a spliced mapping algorithm that first aligns reads to reference transcriptome and genome sequences in an…

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ST Pipeline
Desktop

ST Pipeline

Permits to process and analyze the raw files generated with the Spatial…

Permits to process and analyze the raw files generated with the Spatial Transcriptomics (ST) method. ST Pipeline enables demultiplexing of spatially-resolved RNA-seq data and robust quality filtering…

SPLICIFY
Desktop

SPLICIFY

Identifies differentially expressed splice variants on RNA and protein level.…

Identifies differentially expressed splice variants on RNA and protein level. SPLICIFY is able to identify condition-specific aberrant splicing events on protein level by performing comparative…

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Rail-RNA
Desktop

Rail-RNA

A cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA…

A cloud-enabled spliced aligner that analyzes many samples at once. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is…

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QuasR
Desktop

QuasR

Provides an integrated analysis of high-throughput sequencing data in R,…

Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different…

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Read-Split-Run
Web
Desktop

Read-Split-Run

Processes RNA-Seq data in a more efficient manner with flexible parameters.…

Processes RNA-Seq data in a more efficient manner with flexible parameters. Read-Split-Run is a computational method for identifying non-canonical, possibly very short, splicing regions. This…

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hppRNA
Desktop

hppRNA

Converts the raw fastq files into gene/isoform expression matrix and…

Converts the raw fastq files into gene/isoform expression matrix and differentially expressed genes or isoforms. hppRNA is a one-in-all solution composed of four scenarios such as pre-mapping,…

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RNASEQR
Desktop

RNASEQR

Analyzes raw data from RNA-seq experiments effectively and outputs results in a…

Analyzes raw data from RNA-seq experiments effectively and outputs results in a manner that is compatible with a wide variety of specialized downstream analyses on desktop computers. RNASEQR yields…

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OSA
Desktop

OSA Omicsoft Sequence Aligner

A super-fast and accurate alignment tool for RNA-Seq data. Benchmarked with…

A super-fast and accurate alignment tool for RNA-Seq data. Benchmarked with existing methods, OSA improves mapping speed 4-10 folds with better sensitivity and less false positives.

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Splign
Web

Splign

Computes cDNA-to-Genome alignments. Splign include a high-performance…

Computes cDNA-to-Genome alignments. Splign include a high-performance preliminary alignment, a compartment identification based on a formally defined model of adjacent duplicated regions, and a…

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SePIA
Desktop

SePIA Sequence Processing Integration and Analysis

Automates RNA-seq processing, integration and analysis. SePIA allows…

Automates RNA-seq processing, integration and analysis. SePIA allows reproducible analysis of total RNA, poly(A)-derived RNA, small RNA, and integrated microRNA (miRNA) and mRNA data. It provides a…

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wapRNA
Desktop
Web

wapRNA

This is a free web-based application for the processing of high-throughput…

This is a free web-based application for the processing of high-throughput RNA-Seq data from next generation sequencing (NGS) platforms, such as Genome Analyzer of Illumina Inc. (Solexa) and SOLiD of…

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SpliceSeq
Desktop

SpliceSeq

A tool for investigating alternative mRNA splicing in next generation mRNA…

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…

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Supersplat
Desktop

Supersplat

An application for discovering potential splice junctions in high throughput…

An application for discovering potential splice junctions in high throughput sequencing (HTS) data.

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RNA CoMPASS
Desktop

RNA CoMPASS

A web-based GUI distributed computational pipeline, provides all-in-one…

A web-based GUI distributed computational pipeline, provides all-in-one functionality including human transcriptome quantification and the typical endogenous RNA-Sequencing analysis along with the…

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RNAMiner
Web

RNAMiner

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five…

A multi-level bioinformatics protocol and pipeline. RNAMiner includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed…

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Zika-RNAseq-Pip…
Desktop

Zika-RNAseq-Pipeline

Provides an open source RNA-seq processing pipeline that can be used to extract…

Provides an open source RNA-seq processing pipeline that can be used to extract knowledge from any study that profiled gene expression using RNA-seq applied to mammalian cells, comparing two…

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MetaTrans
Desktop

MetaTrans

Analyzes the structure and functions of active microbial communities using the…

Analyzes the structure and functions of active microbial communities using the power of multi-threading computers. MetaTrans is designed to perform two types of RNA-Seq analyses: taxonomic and gene…

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miARma-Seq
Desktop

miARma-Seq

Designed for mRNA, miRNA and circRNA identification and differential expression…

Designed for mRNA, miRNA and circRNA identification and differential expression analysis, applicable to any sequenced organism. miARma-Seq is presented as a stand-alone tool that provides different…

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RapMap
Desktop

RapMap

An algorithm, quasi-mapping, for mapping sequencing reads to a transcriptome.…

An algorithm, quasi-mapping, for mapping sequencing reads to a transcriptome. By attempting only to report the potential loci of origin of a sequencing read, and not the base-to-base alignment by…

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PASSion
Desktop

PASSion

A pattern growth algorithm based pileline for splice site detection in…

A pattern growth algorithm based pileline for splice site detection in paired-end RNA-Seq data.

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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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TRAP
Desktop
Web

TRAP Time-series RNA-seq Analysis Package

A comprehensive package integrating all necessary tasks such as mapping short…

A comprehensive package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis…

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HMMSplicer
Desktop

HMMSplicer

An accurate and efficient algorithm for discovering canonical and non-canonical…

An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets.

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ContextMap
Desktop

ContextMap

An RNA-seq mapping algorithm that uses a context-based approach to identify the…

An RNA-seq mapping algorithm that uses a context-based approach to identify the best alignment for each read and allows parallel mapping against several reference genomes. Its key novel features are:…

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ABMapper
Desktop

ABMapper

A portable, easy-to-use package for spliced alignment, junction site detection,…

A portable, easy-to-use package for spliced alignment, junction site detection, and reads mapping.

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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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GESS
Desktop

GESS Graph-based Exon-Skipping Scanner

Detects de novo exon-skipping events directly from raw RNA-seq data without…

Detects de novo exon-skipping events directly from raw RNA-seq data without prior knowledge of gene-annotation information. First, we build a splicing-site-linking graph from splicing-aware aligned…

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RAMICS
Desktop
Web

RAMICS Rapid Amplicon Mapping in Codon Space

A hidden Markov model reference mapper, designed to align coding and non-coding…

A hidden Markov model reference mapper, designed to align coding and non-coding DNA to a reference sequence. By default, RAMICS assumes DNA is coding and Sanger-sequenced. Options allow the user to…

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UnSplicer
Desktop

UnSplicer

An RNA-seq alignment program, providing fast and accurate alignment of short…

An RNA-seq alignment program, providing fast and accurate alignment of short reads to a reference genome.

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Portcullis
Desktop

Portcullis

Filters invalid splice junctions (SJs) from BAM alignments produced by any…

Filters invalid splice junctions (SJs) from BAM alignments produced by any RNA-seq mapper. Portcullis provides rich junction analysis and quantification capabilities. It can perform junction file…

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LSTrAP
Desktop

LSTrAP Large-Scale Transcriptome Analysis Pipeline

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality…

Pre-processes RNA-seq data and maps it to the genome. LSTrAP performs quality control and produces co-expression networks. It provides functional and comparative genomics data to enable a host of…

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DART
Desktop

DART Division based Alignment for RNA-Seq Transcripts

Allows RNA-Seq mapping. DART is a Burrows Wheeler Transform (BWT)-based aligner…

Allows RNA-Seq mapping. DART is a Burrows Wheeler Transform (BWT)-based aligner that adopts a partitioning strategy to divide a read into simple pairs (perfect alignments) and normal pairs…

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exceRpt
Web

exceRpt

Allows users to processing of RNA-Seq data. exceRpt is a pipeline for RNA-Seq…

Allows users to processing of RNA-Seq data. exceRpt is a pipeline for RNA-Seq library preparation. The software processes each sample independently through a cascade of read-alignment steps designed…

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zUMIs
Desktop

zUMIs

Processes raw reads to count tables for RNA-seq data using Unique Molecular…

Processes raw reads to count tables for RNA-seq data using Unique Molecular Identifiers (UMIs). zUMIs is a pipeline applicable for most experimental designs of RNA-seq data, such as single-nuclei…

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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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viGEN
Desktop

viGEN

Combines existing well-known and novel RNA-seq tools for not only detection and…

Combines existing well-known and novel RNA-seq tools for not only detection and quantification of viral RNA, but also variants in the viral transcripts. ViGEN includes 4 major modules: the first…

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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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PALMapper
Desktop

PALMapper

Computes both spliced and unspliced alignments at high accuracy while taking…

Computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions.

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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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RAP
Web

RAP RNA-seq Analysis Pipeline

Allows users to analyze sequencing data in multiple steps. The RAP purpose is…

Allows users to analyze sequencing data in multiple steps. The RAP purpose is to investigate the complex transcriptional landscape of eukaryotic transcriptomes through a computationally optimized…

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PASTA
Desktop

PASTA Patterned Alignments for Splicing and Transcriptome Analysis

A modular software pipeline for the analysis of RNA-Sequencing data. PASTA…

A modular software pipeline for the analysis of RNA-Sequencing data. PASTA provides an innovative algorithm for the accurate, unbiased identification of splice junctions; automatic generation of gene…

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Glbase
Desktop

Glbase

Allows the user to perform many common analyses on ChIP-seq, microarray and…

Allows the user to perform many common analyses on ChIP-seq, microarray and RNA-seq data. Glbase is a flexible and multifunctional toolkit which includes many functions to intersect two lists of…

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Disambiguate
Desktop

Disambiguate

Works by operating on natural name sorted BAM files from alignments to two…

Works by operating on natural name sorted BAM files from alignments to two species. Disambiguate provides an important tool for computationally separating sequence reads originating from two species.…

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IRAP
Desktop

IRAP integrated RNA-seq Analysis Pipeline

A flexible RNA-seq analysis pipeline that allows the user to select and apply…

A flexible RNA-seq analysis pipeline that allows the user to select and apply their preferred combination of existing tools for mapping reads, quantifying expression and testing for differential…

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CLASS
Desktop

CLASS Constraint-based Local Assembly and Selection of Splice variants

Identifies low abundance splice variation with high accuracy. CLASS employs a…

Identifies low abundance splice variation with high accuracy. CLASS employs a linear programming method to detect exons. It can select candidate transcripts using an efficient dynamic programming…

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OncoRep
Desktop

OncoRep Oncogenomics Report

A fully automated RNA-Seq based report for patients with (breast) cancer, which…

A fully automated RNA-Seq based report for patients with (breast) cancer, which includes molecular classification, detection of altered genes, detection of altered pathways, identification of gene…

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SpliceJumper
Desktop

SpliceJumper

Consists in a classification based approach for calling splicing junctions from…

Consists in a classification based approach for calling splicing junctions from RNA-seq data. SpliceJumper uses a machine learning approach that combines multiple features extracted from RNA-seq…

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SPARTA
Desktop

SPARTA

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a…

Extracts raw Illumina reads to differentially expressed genes. SPARTA is a bacterial RNA-seq analysis tool performing transcriptional profiling experiments using RNA-seq. It enables microbiologists…

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SeqSaw
Desktop

SeqSaw

A package for mapping of spliced reads and unbiased detection of novel splice…

A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

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RSW
Desktop

RSW Read-Split-Walk

A spliced region detection pipeline designed to identify non-canonical,…

A spliced region detection pipeline designed to identify non-canonical, possibly very short, splicing regions using RNA-Seq data. RSW is a practical approach for identifying non-canonical splice…

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JAGuaR
Desktop

JAGuaR

An alignment protocol for RNA-seq reads that uses an extended reference to…

An alignment protocol for RNA-seq reads that uses an extended reference to increase alignment sensitivity. JAGuaR uses BWA to align reads to the genome and reference transcript models (including…

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SplicingGraphs
Desktop

SplicingGraphs

Allows the user to create, manipulate, and visualize splicing graphs and their…

Allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. SplicingGraphs is a Bioinformatic package that permits to assign…

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r-make
Desktop

r-make

A pipeline that processes RNA sequencing reads. r-make estimates the expression…

A pipeline that processes RNA sequencing reads. r-make estimates the expression levels for exons, genes, and splice junctions. In the process, it prints a range of quality metrics and statistics,…

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GMAP
Desktop

GMAP

Maps and aligns a single sequence with minimal startup time and memory…

Maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. GMAP is a standalone program for mapping and aligning…

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SLaP mapper
Web

SLaP mapper Spliced-Leader and Polyadenlyation site mapper

A fully automated web-service for identification, quantification and…

A fully automated web-service for identification, quantification and gene-assignment of both spliced-leader and polyadenylation addition sites in Kinetoplastid genomes. SLaP mapper only requires raw…

CAFTAN
Web
Desktop

CAFTAN

Offers high-throughput cDNA analyzes. CAFTAN allows users to rank the sequences…

Offers high-throughput cDNA analyzes. CAFTAN allows users to rank the sequences according to their potential to be derived from both complete transcripts and spliced forms. The software is available…

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HSA
Desktop

HSA

Performs splice alignment for RNA-Seq data. HSA first divides the input reads…

Performs splice alignment for RNA-Seq data. HSA first divides the input reads in equal segments that are aligned and mapped. Then, the application filters the segments based on mapping results and…

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Torrent Suite…
Server

Torrent Suite Software

Provides a platform for handling various data analysis. Torrent Suite Software…

Provides a platform for handling various data analysis. Torrent Suite Software is composed of four mains modules that authorizes: (i) to create a run plan downloadable directly to the sequencer; (ii)…

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Hera
Desktop

Hera

Helps to analyze RNA-seq data. Hera is a bioinformatics software that provides…

Helps to analyze RNA-seq data. Hera is a bioinformatics software that provides (i) base-to-base alignment BAM file, (ii) transcript abundance estimation, and (iii) fusion gene detection with fused…

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RiboPip
Desktop

RiboPip

Enables users to process Ribosome Profiling (Ribo-seq) and RNA sequencing…

Enables users to process Ribosome Profiling (Ribo-seq) and RNA sequencing (RNA-seq) datasets. RiboPip computes a splice-aware alignment to a reference database along with a read summarization and…

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BBMap
Desktop

BBMap

Uses as a splice-aware aligner for short and long reads. BBMap is shown to be a…

Uses as a splice-aware aligner for short and long reads. BBMap is shown to be a fast and accurate aligner, capable of correctly handling an overall wider variety of references, reads, and mutations…

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Partek Flow
Desktop

Partek Flow

Enable researchers to self-sufficiently perform data analysis. Partek Flow…

Enable researchers to self-sufficiently perform data analysis. Partek Flow software is designed specifically for the analysis needs of next generation sequencing (NGS) applications including RNA,…

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AIR
Web

AIR Artificial intelligence RNAseq

Offers a solution to close the gap between data production and data…

Offers a solution to close the gap between data production and data interpretation, making it possible for researchers to do their own analysis in the simplest possible way and giving them the…

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QRNAseq
Desktop

QRNAseq

A tool to manage huge amounts of RNA-seq data in an integrative way which…

A tool to manage huge amounts of RNA-seq data in an integrative way which includes RNA-seq data quality control, read alignment, gene fusion, gene mutation, isoform identification and function…

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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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MapAl
Desktop

MapAl

A tool for RNA-Seq expression profiling that builds on the established programs…

A tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. In the post-processing of RNA-Seq reads, it incorporates gene models already at the stage of read…

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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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Array Studio
Desktop

Array Studio

Provides the premier enterprise solution for data content, framework and…

Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server)…

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RobiNA
Desktop

RobiNA

A User Friendly Graphical Interface to Powerful Open Source Microarray and…

A User Friendly Graphical Interface to Powerful Open Source Microarray and RNA-Seq Processing.

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X-MATE
Desktop

X-MATE

Provides a pipeline for the recursive mapping of RNA-seq datasets. X-MATE is an…

Provides a pipeline for the recursive mapping of RNA-seq datasets. X-MATE is an updated version of RNA-MATE, capable of mapping both RNA-seq and DNA datasets and with different configuration files.…

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SOAPsplice
Desktop

SOAPsplice

A tool for genome-wide ab initio detection of splice junction sites from…

A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA.

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IsoformEx
Desktop

IsoformEx

A fast and accurate algorithm to estimate transcript expression levels and gene…

A fast and accurate algorithm to estimate transcript expression levels and gene expression levels, which takes into account short exons and alternative exons with a weighting scheme. IsoformEx…

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MapNext
Desktop

MapNext

A software tool for both spliced and unspliced alignments of short sequence…

A software tool for both spliced and unspliced alignments of short sequence reads onto reference sequences, and automated SNP detection using neighbourhood quality standards. MapNext provides four…

G T A T C G C T A
Xenome
Desktop

Xenome

Performs fast, accurate and specific classification of xenograft-derived…

Performs fast, accurate and specific classification of xenograft-derived sequence read data. Xenome technique is based on a k-mer decomposition of the host and graft reference sequences. It has been…

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