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Software pipelines (small RNA-seq analysis)

These software pipelines provide out-of-the box solutions for small RNA sequencing analysis by combining a number of specific analysis programs together.

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mirTools
Web

mirTools

An integrated web server was developed to investigate ncRNA sequences,…

An integrated web server was developed to investigate ncRNA sequences, expression levels, differentially expressed ncRNAs and miRNA-targeted genes and their functional annotation, which will be…

oneChannelGUI
Desktop

oneChannelGUI

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops.…

Facilitates analysis of microarrays and miRNA/RNA-seq data on laptops. oneChannelGUI can be used for quality control, normalization, filtering, statistical validation and data mining for single…

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sRNAtoolbox
Web

sRNAtoolbox

A collection of small RNA analysis tools. sRNAtoolbox is aimed to provide small…

A collection of small RNA analysis tools. sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and…

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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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CPSS
Web

CPSS Computational Platform for analysis of Small RNA deep Sequencing data

Provides a comprehensive integrated pipeline for analyzing small RNA deep…

Provides a comprehensive integrated pipeline for analyzing small RNA deep sequencing data. CPSS delivers analysis report from ncRNA quantification to miRNA target prediction and annotation of single…

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DARIO
Web

DARIO

A free web service that allows to study short read data from small RNA-seq…

A free web service that allows to study short read data from small RNA-seq experiments. DARIO provides a wide range of analysis features, including quality control, read normalization, ncRNA…

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UEA sRNA…
Desktop

UEA sRNA toolkit

This site provides access to our software tools for the analysis of…

This site provides access to our software tools for the analysis of high-throughput small RNA data.

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SeqBuster
Desktop

SeqBuster

Permits users to analyse small RNA data from Illumina sequencing. SeqBuster is…

Permits users to analyse small RNA data from Illumina sequencing. SeqBuster is a web-based bioinformatic tool providing an automatized pre-analysis for sequence annotation. This software offers a…

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CANEapp
Desktop

CANEapp Comprehensive automated Analysis of Next-generation sequencing Experiments

Integrates data from different sources and experiments. CANEapp is a platform…

Integrates data from different sources and experiments. CANEapp is a platform for integrating next-generation sequencing (NGS) analysis pipelines and tools into a user-friendly suite that can be…

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miRNAKey
Desktop

miRNAKey

Allows to analyse microRNA deep sequencing data. miRNAKey is designed to be…

Allows to analyse microRNA deep sequencing data. miRNAKey is designed to be used as a base station for the analysis of miRNA sequencing data. The main steps include: (i) searching for and removing…

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TRAPLINE
Desktop

TRAPLINE Transparent Reproducible and Automated PipeLINE

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides…

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides researchers through the NGS data analysis process in a transparent and automated state-of-the-art pipeline. It can detect…

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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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ncPRO-seq
Desktop

ncPRO-seq

It aims to interrogate and perform detailed analysis on small RNAs derived from…

It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions.

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ISRNA
Web

ISRNA Integrative Short Reads NAvigator

A piece of online software designed for storage, visualization and analysis of…

A piece of online software designed for storage, visualization and analysis of small RNA sequencing data produced by high-throughput sequencing technologies. Besides the high-speed genome mapping…

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MIRPIPE
Desktop
Web

MIRPIPE

Allows rapid and simple browser-based miRNA homology detection and…

Allows rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing…

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isomiRex
Web

isomiRex

An effective platform for the identification and the visualization of miRNAs…

An effective platform for the identification and the visualization of miRNAs and their cognate isomiRs using NGS datasets spanning 193 species (including plants, animals and viruses using miRbase…

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miFRame
Web

miFRame

Performs quantification of expression on miRNA precursors and mature forms of…

Performs quantification of expression on miRNA precursors and mature forms of miRNAs, and allows for discovering differentially expressed markers. miFRame is a software for the analysis of single…

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iMir
Desktop

iMir

A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising…

A modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, DE analysis, target prediction by integrating multiple open…

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shortran
Desktop

shortran

A pipeline designed to analyse RNA sequencing data by producing graphical and…

A pipeline designed to analyse RNA sequencing data by producing graphical and MySQL output. Nine different steps of analyses are possible, ranging from trimming to annotation or pattern search. The…

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plantDARIO
Web

plantDARIO

Provides many basic features of a small RNA-seq analysis, including quality…

Provides many basic features of a small RNA-seq analysis, including quality control, read normalization, short non-coding RNAs, particularly focused on plants. plantDARIO provides data for A.…

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miRdentify
Desktop

miRdentify

Identifies MicroRNAs (miRNA) in animals. miRdentify is a miRNA prediction…

Identifies MicroRNAs (miRNA) in animals. miRdentify is a miRNA prediction strategy that, based on gradual increase in 10 parameters, ensures a selection of highly miRNA-like hairpin structures. The…

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sRNAnalyzer
Desktop

sRNAnalyzer

Identifies bacterial species from sample. sRNAnalyzer is a customizable small…

Identifies bacterial species from sample. sRNAnalyzer is a customizable small RNA analysis pipeline for next generation sequencing (NGS) data. It uses a dataset of plasma samples from CRC patients to…

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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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Smallrnaseq
Desktop

Smallrnaseq

Can quantify and analyze small non-coding RNA species (sncRNAs). Smallrnaseq…

Can quantify and analyze small non-coding RNA species (sncRNAs). Smallrnaseq allows general analysis of small RNAs and not just miRNAs. It can be integrated into another platform thank to the…

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AASRA
Desktop

AASRA Anchor Alignment-Based Small RNA Annotation

Annotates sncRNA. AASRA is based on a unique anchor alignment algorithm which…

Annotates sncRNA. AASRA is based on a unique anchor alignment algorithm which avoids repetitive or ambiguous counting. It is able to differentiate mature miRNA from precursor miRNA reads. The tool is…

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mirPRo
Desktop

mirPRo

Quantifies known miRNAs and predicts novel miRNAs. Compared with the most…

Quantifies known miRNAs and predicts novel miRNAs. Compared with the most widely used standalone program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome…

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Chimira
Web

Chimira

An online tool for analysing large amounts of small RNA-Seq data and acquiring…

An online tool for analysing large amounts of small RNA-Seq data and acquiring their modifications profile. It allows the mapping of the input sequences to miRBase in order to decipher the miRNA…

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Oasis
Web

Oasis

A web application that allows for the fast and flexible online analysis of…

A web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. Oasis was designed for the end user in the lab, providing an easy-to-use web frontend…

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FlaiMapper
Desktop

FlaiMapper Fragment Location Annotation Identification Mapper

A method that extracts and annotates the locations of sncRNA-derived RNAs…

A method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs). These sncdRNAs are often detected in sequencing data and observed as fragments of their precursor sncRNA. Using…

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BioVLAB-MMIA-NG…
Desktop

BioVLAB-MMIA-NGS

A system for MicroRNA-MRNA integrated analysis using high throughput sequencing…

A system for MicroRNA-MRNA integrated analysis using high throughput sequencing data by utilizing cloud computing environment.

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LimiTT
Web

LimiTT

A web-based pipeline which can automatically identify and link validated miRNA…

A web-based pipeline which can automatically identify and link validated miRNA target interactions (MTIs) from extensive lists of miRNAs and target genes in batch mode, even if the provided data is…

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PIPmiR
Desktop

PIPmiR

A pipeline to identify novel plant miRNA genes from a combination of deep…

A pipeline to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features. PIPmiR uses a probabilistic model that combines RNA structure and expression…

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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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miRge
Desktop

miRge

A logical, ultrafast, small RNA-seq solution to process samples in a highly…

A logical, ultrafast, small RNA-seq solution to process samples in a highly multiplexed fashion, resulting in dramatically decreased computational requirements when processing sets of samples in a…

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MAGI
Web

MAGI

A web service for fast MicroRNA-Seq data analysis in a GPU infrastructure.

A web service for fast MicroRNA-Seq data analysis in a GPU infrastructure.

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eRNA
Desktop

eRNA

Focuses on the common tools required for the mapping and quantification…

Focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. eRNA provides an additional choice for scientists who require a user-friendly…

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CAP-miRSeq
Desktop

CAP-miRSeq Comprehensive Analysis Pipeline for microRNA Sequencing data

Integrates read pre-processing, alignment, mature/precursor/novel miRNA…

Integrates read pre-processing, alignment, mature/precursor/novel miRNA detection and quantification, data visualization, variant detection in miRNA coding region, and more flexible differential…

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SMiRK
Desktop

SMiRK

A software pipeline for rapid processing and analysis of data from…

A software pipeline for rapid processing and analysis of data from high-throughput miRNA sequencing experiments. Features of SMiRK include adaptor trimming, alignment, normalization, data…

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iSRAP
Desktop

iSRAP integrated Small RNA Analysis Pipeline

A one-touch integrated small RNA analysis pipeline (iSRAP) research tool that…

A one-touch integrated small RNA analysis pipeline (iSRAP) research tool that is composed of widely used tools for rapid profiling of small RNAs. The performance test of iSRAP using publicly and…

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SiLoCo
Desktop

SiLoCo Short interfering RNA Locus Comparison

Identifies sRNA loci on plant genomes from two sRNA datasets, which can be…

Identifies sRNA loci on plant genomes from two sRNA datasets, which can be uploaded by the user or selected from publicly available datasets. SiLoCo maps sRNA sequences to the genome using PatMaN and…

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Genecopoeia
Dataset

Genecopoeia

Provides genomics and proteomics products and services for academic and…

Provides genomics and proteomics products and services for academic and governmental research institutes, pharmaceutical and biotechnology industry. Genecopoeia, Inc. is a US-based manufacturer that…

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tsRFinder
Desktop

tsRFinder

A lightweight, fast and reliable tool for prediction and annotation of…

A lightweight, fast and reliable tool for prediction and annotation of tRNA-derived small RNAs (tsRNA, tRF) using next-generation sequencing data.

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Rosetta…
Desktop

Rosetta software suite

Offers methods for structure prediction, design, and remodeling of proteins and…

Offers methods for structure prediction, design, and remodeling of proteins and nucleic acids. Rosetta provides a comprehensive software suite for modeling macromolecular structures. This resource…

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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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Strand NGS
Desktop

Strand NGS

Provides analysis, management and visualization tools for next-generation…

Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq,…

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DSAP
Web

DSAP

An automated multiple-task web service designed to provide a total solution to…

An automated multiple-task web service designed to provide a total solution to analyzing deep-sequencing small RNA datasets generated by next-generation sequencing technology. DSAP uses a…

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miRGator
Dataset

miRGator

Aims to be the microRNA (miRNA) portal encompassing microRNA diversity,…

Aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression profiles, target relationships, and various supporting tools. By keeping datasets and analytic tools up-to-date,…

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miRDeepFinder
Desktop

miRDeepFinder

Provides an comprehensive workflow of analyzing data from plant microRNA…

Provides an comprehensive workflow of analyzing data from plant microRNA (miRNA) deep sequencing.

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SoMART
Web

SoMART Solanaceae miRNA/tasiRNA Analysis Resources and Tools

Helps users to characterize tasiRNA genes. SoMART is a web server that consists…

Helps users to characterize tasiRNA genes. SoMART is a web server that consists of four online tools and four types of databases. The tools include (i) Slicer detector, (ii) dRNA mapper, (iii) PreMIR…

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E-miR
Desktop

E-miR

An easy to use perl-based analysis pipeline to handle sequencing data in…

An easy to use perl-based analysis pipeline to handle sequencing data in several automated steps including data format conversion, 3' adapter removal, genome alignment and annotation to…

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