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# Name Description Online/Local Organism
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Features References
1 BioVLAB-MMIA-NGS BioVLAB-MMIA-NGS is Cloud-based miRNA mRNA integraed analysis system using NGS data. System computes differentially/significantly expressed miRNAs (DEmiRNAs) and mRNAs/genes (DEGs), and with targeting information, DEGs targeted by DEmiRNAs and having negative correlation between them are extracted. /
  • human
  • mice
  • macaca
  • plants (rice)
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • precursor prediction
  • Homepage

    Publication
    Sept. 29, 2014
    Citations: 5
    2 CAP-miRSeq Comprehensive analysis pipeline for deep microRNA sequencing (CAP-miRSeq) integrates read preprocessing, alignment, mature/precursor/novel miRNA qualification, variant detection in miRNA coding region, and flexible differential expression between experimental conditions. According to computational infrastructures, users can run samples sequentially or in parallel for fast processing. In either a case, summary and expression reports for all samples are generated for easier quality assessment and downstream analyses. /
  • any (from miRBase)
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • precursor prediction
  • other ncRNA identification
  • Homepage

    Publication
    June 3, 2014
    Citations: 44
    3 Chimira Chimira is a web-based system for miRNA analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3′-modifications, 5′-modifications and also internal modifications or variation. /
  • any (from miRBase)
  • known miRNA identification
  • differential expression
  • Homepage

    Publication
    June 20, 2015
    Citations: 21
    4 CleaveLand4 CleaveLand a generalizable computational pipeline for the detection of cleaved miRNA targets from degradome data. CleaveLand takes as input degradome sequences, small RNAs and an mRNA database and outputs small RNA targets. /
  • any
  • target prediction
  • Homepage

    Publication
    Nov. 18, 2008
    Citations: 143
    5 CPSS CPSS is (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • other animals (selectable)
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • precursor prediction
  • isomiRs identyfication
  • other ncRNA identification
  • Homepage

    Publication
    May 9, 2012
    Citations: 18
    6 DARIO A free web server for the analysis of short RNAs from high-throughput sequencing data. /
  • human
  • monkey
  • mouse
  • rat
  • fly
  • worm
  • fish
  • novel miRNA Identification
  • known miRNA identification
  • other ncRNA identification
  • Homepage

    Publication
    May 27, 2011
    Citations: 26
    7 DeAnnIso DeAnnIso, is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data. The detected isomiRs will be classified into different categories. The isomiRs will be aligned with canonical miRNA, and will be annotated with expression, constitution, SNP, and an in-house dataset. It can also extract differentially expressing isomiR between two samples. In addition, IsomiR Bank provides targets prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. /
  • human
  • mouse
  • fish
  • fly
  • plants (selectable)
  • differential expression
  • target prediction
  • target annotation
  • isomiRs identyfication
  • Homepage

    Publication
    May 13, 2016
    Citations: 7
    8 eRNA eRNA focuses on the common tools required for the mapping and quantification analysis of miRNA-seq and mRNA-seq data. The software package provides an additional choice for scientists who require a user-friendly computing environment and high-throughput capacity for large data analysis. /
  • any
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • precursor prediction
  • Homepage

    Publication
    March 5, 2014
    Citations: 8
    9 iMir iMir is a modular pipeline for comprehensive analysis of smallRNA-Seq data, comprising specific tools for adapter trimming, quality filtering, differential expression analysis, biological target prediction and other useful options by integrating multiple open source modules and resources in an automated workflow. /
  • any
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • precursor prediction
  • isomiRs identyfication
  • other ncRNA identification
  • Homepage

    Publication
    Dec. 13, 2013
    Citations: 19
    10 isomiR2Function somiR2Function allows for the high-throughput detection of plant isomiRs from any miRNA-seq profiling study. isomiR2Function not only allows for the identification of the templated and non-templated 5′- isomiRs and 3′- isomiRs but also allows for the expression quantification. Since, the prediction of biologically relevant target is an important criterion for the identification of isomiRs and their targets - isomiR2Function identifies target as well. Following target prediction, it allows for functional enrichment of the identified targets. In parallel, isomiR2Function provides support for the visualization of read mapping on corresponding precursor sequences. /
  • plants
  • differential expression
  • target prediction
  • target annotation
  • isomiRs identyfication
  • Homepage

    Publication
    March 21, 2017
    Citations: 0
    11 IsomiRage A workflow for the characterization and analysis of miRNAs and their variants in next-generation sequencing datasets. IsomiRage permits the deconvolution of miRNA heterogeneity and could be used to explore the functional role of miRNA isoforms. /
  • any
  • known miRNA identification
  • isomiRs identyfication
  • Homepage

    Publication
    Sept. 29, 2014
    Citations: 20
    12 isomiReX IsomiRex is a open-access web platform to identify isomiRs and on the fly graphical visualization of the differentially expressed miRNAs in control as well as treated library. /
  • any
  • known miRNA identification
  • differential expression
  • isomiRs identyfication
  • Homepage

    Publication
    July 4, 2013
    Citations: 14
    13 LeARN/smallA A platform based on LeARN, dedicated to analyse data generated by RNAseq small RNA projects. /
  • any
  • known miRNA identification
  • target prediction
  • precursor prediction
  • other ncRNA identification
  • Homepage

    Publication
    Jan. 14, 2008
    Citations: 8
    14 MAGI MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours—>600% end-to-end performance improvement over state of the art. /
  • human
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • precursor prediction
  • other ncRNA identification
  • Homepage

    Publication
    June 6, 2014
    Citations: 8
    15 miR-PREFeR MiR-PREFeR uses expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species. /
  • plants
  • novel miRNA Identification
  • known miRNA identification
  • Homepage

    Publication
    June 14, 2014
    Citations: 16
    16 miRA miRA is a new tool to identify miRNA precursors in plants, allowing for heterogeneous and complex precursor populations. miRA requires small RNA sequencing data and a corresponding reference genome, and evaluates precursor secondary structures and precursor processing accuracy; key parameters can be adapted based on the specific organism under investigation. /
  • plants
  • novel miRNA Identification
  • precursor prediction
  • Homepage

    Publication
    Nov. 5, 2015
    Citations: 8
    17 miRge miRge is 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 single run. It utilizes a unique sequential alignment algorithm for annotation of small RNA-seq data. Output is given for miRNAs as raw reads and reads per million (RPM) in addition to isomiR data and reads for all other RNA species (tRNA, rRNA, snoRNA, mRNA). IsomiR entropy can be determined for each sample or across samples in a multiplex run. /
  • any
  • known miRNA identification
  • isomiRs identyfication
  • other ncRNA identification
  • Homepage

    Publication
    Nov. 16, 2015
    Citations: 20
    18 miRanalyzer miRanalyzer – a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. /
  • human
  • mouse
  • rat
  • fly
  • worm
  • chicken
  • fish
  • other animals (selectable)
  • plants (selectable)
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • precursor prediction
  • isomiRs identyfication
  • other ncRNA identification
  • Homepage

    Publication
    April 22, 2011
    Citations: 112
    19 miRDeep-P miRDP can be used to identify miRNA genes in plant species, even for those without detailed annotation. It is also designed to assign expression status to individual miRNA genes, which is critical as more miRNAs in plants belong to paralogous families with multiple members encoding identical or near-identical miRNAs. /
  • plants
  • novel miRNA Identification
  • known miRNA identification
  • precursor prediction
  • Homepage

    Publication
    July 19, 2011
    Citations: 64
    20 miRDeep2 miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades /
  • any (from miRBase)
  • novel miRNA Identification
  • known miRNA identification
  • precursor prediction
  • Homepage

    Publication
    Sept. 12, 2011
    Citations: 455
    21 miRdentify A stringent approach to confidently predict novel miRNAs in animals. /
  • animals
  • novel miRNA Identification
  • known miRNA identification
  • Homepage

    Publication
    July 22, 2014
    Citations: 4
    22 MIREAP MIREAP combines small RNA position and depth with a model of microRNA biogenesis to discover microRNAs from deeply sequenced small RNA library. /
  • any
  • novel miRNA Identification
  • known miRNA identification
  • precursor prediction
  • Homepage

    Publication
    23 MIReNA MIReNA looks for miRNA sequences by exploring a multidimensional space defined by only five (physical and combinatorial) parameters characterizing acceptable pre-miRNAs. MIReNA validates pre-miRNAs with high sensitivity and specificity, and detects new miRNAs by homology from known miRNAs or from deep sequencing data. /
  • plants
  • animals
  • known miRNA identification
  • precursor prediction
  • Homepage

    Publication
    June 30, 2010
    Citations: 50
    24 miRExpress A stand-alone software package implemented for generating miRNA expression profiles from high-throughput sequencing of RNA without the need for sequenced genomes. /
  • any (from miRBase)
  • known miRNA identification
  • Homepage

    Publication
    Oct. 12, 2009
    Citations: 84
    25 miRNA Digger miRNA Digger was developed for systematical discovery of miRNA candidates through genome-wide screening of cleavage signals based on degradome sequencing data. /
  • any (from miRBase)
  • novel miRNA Identification
  • Homepage

    Publication
    Jan. 6, 2016
    Citations: 0
    26 miRNAkey miRNAkey is a software package designed to be used as a base-station for the analysis of miRNA deep sequencing data. It implements common steps taken in the analysis of such data, as well as adds unique features, such as data statistics and multiple mapping levels, generating a novel platform for the analysis of miRNA expression. The tabular and graphical output contains detailed reports on the sequence reads and provides an accurate picture of the differentially expressed miRNAs in paired samples. /
  • any (from miRBase)
  • known miRNA identification
  • differential expression
  • Homepage

    Publication
    Aug. 27, 2010
    Citations: 35
    27 MIRPIPE MIRPIPE represents a new pipeline for the quantification of microRNA based on smallRNA sequencing reads. In opposition to present algorithms that generally rely on genomic data to identify miRNAs, MIRPIPE focuses on niche model organisms that lack such information. Among the MIRPIPE features are automatic trimming and adapter removal of raw RNA-Seq reads originating from various sequencing instruments, clustering of isomiRs, and quantification of detected miRNAs by homology search versus public or user uploaded reference databases. /
  • human
  • mouse
  • fly
  • fish
  • chicken
  • rat
  • any
  • known miRNA identification
  • isomiRs identyfication
  • Homepage

    Publication
    Aug. 26, 2016
    Citations: 8
    28 miRPlant The objective of miRPlant program is to predict novel plant miRNA, while providing a user-friendly interface with improved accuracy of prediction. miRPlant does not require any third party tools such as mapping or RNA secondary structure prediction tools. /
  • plants
  • novel miRNA Identification
  • known miRNA identification
  • precursor prediction
  • Homepage

    Publication
    Aug. 12, 2014
    Citations: 17
    29 mirPRo mirPRo is a tool for miRNA-seq analysis. It can quantify known and novel miRNAs in single-end RNA-seq data and provide useful functions such as IsomiR detection and "arm switching" identification, miRNA family quantification, and read cataloging in terms of genome annotation. mirPRo only works for species that has reference genome. /
  • any
  • novel miRNA Identification
  • known miRNA identification
  • precursor prediction
  • isomiRs identyfication
  • Homepage

    Publication
    Oct. 5, 2015
    Citations: 2
    30 miRSeqNovel An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. /
  • plants
  • animals
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • precursor prediction
  • isomiRs identyfication
  • Homepage

    Publication
    May 17, 2012
    Citations: 4
    31 miRTarCLIP From miRTarCLIP scratch, it automatically removes adaptor sequences from raw reads, filters low quality reads, reverts C to T, aligns reads to 3'UTRs, scans for read clusters, identifies high confidence miRNA target sites, and provides annotations from external databases. With multi-threading techniques and our novel C to T reversion procedure, miRTarCLIP greatly reduces the running time comparing to conventional approaches. /
  • human
  • mouse
  • target prediction
  • Homepage

    Publication
    Jan. 21, 2013
    Citations: 18
    32 mirTools 2.0 MirTools 2.0 is updated version of mirTools, which was developed to comprehensive characterize the small RNA transcriptome obtained from high-throughput sequencing. It enables user to: detect and profile non-coding RNA (tRNA, snRNA, snoRNA, rRNA ans piRNA); obtain detailed annotation ifmromation about known miRNA (absolute/realtive reds count and most abundant tags); identify the microRNA targeted genes and their detailed functional annotate; perform the comparison of many samples and identify the differentially expressed non-coding RNAs between experimental groups; discovery the novel miRNAs. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • worm
  • fly
  • other animals (selectable)
  • plants (selectable)
  • any (local)
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • precursor prediction
  • isomiRs identyfication
  • other ncRNA identification
  • Homepage

    Publication
    May 29, 2013
    Citations: 26
    33 MTide MTide is an integrated pipeline designed to parse sRNA-seq and degradome data for miRNA-target identification in plant. It can quantify the known miRNA expression and identify novel miRNA from sRNA-seq data, identify the target of miRNA from degradome data signature, predict target of miRNA precisely, prioritize predicted target according to GO similarity to known or validated target, and identify the expressed miRNA between two samples. /
  • plants
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • precursor prediction
  • Homepage

    Publication
    Sept. 24, 2014
    Citations: 14
    34 ncPRO-seq ncPRO-seq is a tool for annotation and profiling of ncRNAs using deep-sequencing data. This comprehensive and flexible ncRNA analysis pipeline, aims in interrogating and performing detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO-seq pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. /
  • human
  • mouse
  • worm
  • fly
  • Arabidopsis
  • any (local)
  • known miRNA identification
  • other ncRNA identification
  • Homepage

    Publication
    Oct. 7, 2012
    Citations: 27
    35 Oasis 2.0 Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. Oasis’ exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. /
  • human
  • mouse
  • fly
  • fish
  • worm
  • chicken
  • rat
  • other animals (selectable)
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • precursor prediction
  • other ncRNA identification
  • Homepage

    Publication
    Feb. 19, 2015
    Citations: 19
    36 Omics Pipe A computational framework that automates multi-omics data analysis pipelines on high performance compute clusters and in the cloud. It supports best practice published pipelines for RNA-seq, miRNA-seq, Exome-seq, Whole Genome sequencing, ChIP-seq analyses and automatic processing of data from The Cancer Genome Atlas (TCGA). Omics Pipe provides researchers with a tool for reproducible, open source and extensible next generation sequencing analysis. /
  • any
  • known miRNA identification
  • differential expression
  • Homepage

    Publication
    Jan. 30, 2015
    Citations: 15
    37 PIPmir PIPmiR is a algorithm to identify novel plant miRNA genes from a combination of deep sequencing data and genomic features. The algorithm can be used as the full pipeline, as just a classifier, or as just a plant precursor sequence predictor. /
  • plants
  • novel miRNA Identification
  • known miRNA identification
  • precursor prediction
  • Homepage

    Publication
    Sept. 22, 2011
    Citations: 38
    38 plantDARIO plantDARIO is a free web service focussing on the analysis of short-read data from small RNA-seq experiments in plants. It provides basic features including quality control, read normalization, ncRNA quantification, and prediction of putative novel ncRNAs. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered. /
  • plants
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • other ncRNA identification
  • Homepage

    Publication
    Dec. 23, 2014
    Citations: 3
    39 QuagmiR QuagmiR - the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designated for the detection and annotation of isomiRs of heterogeneous nature. It permits extensive customization of the query process and reference databases to meet the user’s diverse demands. QuagmiR is written in Python and can be obtained freely from Github. QuagmiR can be run from command-line on local machines, as well as high performance servers. A web-accessible version of the tool has also been made available for use by academic researchers through the National Cancer Institute-funded Seven Bridges Cancer Genomics Cloud. /
  • Invertebrates
  • plants
  • Vertebrates
  • viruses
  • animals
  • mouse
  • fish
  • worm
  • rat
  • fly
  • human
  • chicken
  • any
  • known miRNA identification
  • isomiRs identyfication
  • other ncRNA identification
  • Homepage

    Publication
    40 RandA RandA is a tool for deep-sequencing data analysis. It performs various RNA-seq analysis steps including: adapter clipping; alignment against a database derived from Rfam; multiple mapping handling; read count normalization and differential expression testing for each transcript detected in the samples. /
  • any (from Rfam)
  • known miRNA identification
  • differential expression
  • other ncRNA identification
  • Homepage

    Publication
    March 9, 2012
    Citations: 6
    41 SeqBuster A command-line bioinformatic tool usefull for the analysis of deep sequencing data, namely known miRNAs and isomiRs annotation. /
  • any
  • known miRNA identification
  • isomiRs identyfication
  • Homepage

    Publication
    Dec. 11, 2009
    Citations: 60
    42 shortran Shortran provides an efficient and user-friendly tool for flexible analysis of sRNA-seq data. Using shortran, user is able to quickly generate and combine annotation and profiling information from a complex sRNA-seq experiment. /
  • plants
  • animals
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • Homepage

    Publication
    Aug. 22, 2012
    Citations: 7
    43 sPARTA A powerful tool for plant miRNA target prediction and PARE validation. It can search for targets in unannotated genomic regions, which is useful to discover novel regulatory modules, independent of genome annotations that may be incomplete. /
  • plants
  • target prediction
  • Homepage

    Publication
    Aug. 12, 2014
    Citations: 14
    44 sRNAtoolbox sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools. The center piece of sRNAtoolbox is sRNAbench, which allows the expression profiling and prediction of novel microRNAs in deep sequencing experiments. The other tools can be either launched on sRNAbench results, or independently using the appropriate file formats. /
  • human
  • mouse
  • rat
  • chicken
  • fly
  • fish
  • viruses
  • plants (selectable)
  • bacteria
  • other animals (selectable)
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • isomiRs identyfication
  • other ncRNA identification
  • Homepage

    Publication
    May 27, 2015
    Citations: 44
    45 UEA sRNA Workbench The UEA sRNA workbench is a simple to use, downloadable sRNA software package based on algorithms developed for the original UEA sRNA Toolkit that will perform a complete analysis of single or multiple-sample small RNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel micro RNA sequences) or other tasks such as profiling small RNA expression patterns in genetic data. /
  • plants
  • animals
  • viruses
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • precursor prediction
  • other ncRNA identification
  • Homepage

    Publication
    May 24, 2012
    Citations: 87
    46 wapRNA wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content. wapRNA provides researchers with efficient ways to measure RNA sequence experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions, annotate the known miRNAs or predict the news and so on.  /
  • human
  • mouse
  • rat
  • worm
  • fly
  • chicken
  • worm
  • fish
  • other animals (selectable)
  • any (local)
  • novel miRNA Identification
  • known miRNA identification
  • differential expression
  • target prediction
  • target annotation
  • precursor prediction
  • other ncRNA identification
  • Homepage

    Publication
    Sept. 6, 2011
    Citations: 23