| # | Name | Description | Online/Local | Organism Specific |
NGS Data Needed | Reference Genome Needed |
References |
|---|---|---|---|---|---|---|---|
| 1 | 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. | / |
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Homepage Publication May 9, 2012 Citations: 25 | ||
| 2 | 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. | / |
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Homepage Publication May 13, 2016 Citations: 20 | ||
| 3 | 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. | / |
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Homepage Publication March 21, 2017 Citations: 11 | ||
| 4 | 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. | / |
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Homepage Publication Sept. 29, 2014 Citations: 40 | ||
| 5 | 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. | / |
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Homepage Publication Aug. 26, 2016 Citations: 11 | ||
| 6 | 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. | / |
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Homepage Publication Oct. 5, 2015 Citations: 22 | ||
| 7 | miRSeqNovel | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. | / |
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Homepage Publication May 17, 2012 Citations: 7 | ||
| 8 | 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. | / |
(online) (local) |
Homepage Publication May 29, 2013 Citations: 40 | ||
| 9 | Prost! | Prost! (PRocessing Of Short Transcripts) analyzes any source of smallRNA sequencing data. Prost! does not rely on existing annotation to filter sequencing reads but instead starts by aligning all the reads on a user-provided genomic reference, allowing the study of miRNAs in any species. Additionally, any number of samples can be studied together in a single Prost! run, allowing a more accurate analysis of an entire dataset. After grouping the processed reads by genomic location, Prost! then annotates the reads using a user-defined annotation database (public or personal annotation database). Genomic alignment, grouping, and then annotation enable the study of potentially novel miRNAs, as well as permitting the retention of all the isomiRs that a miRNA may display. Finally Prost! contains additional features such as grouping by seed sequence for a more functional approach of the dataset, provides automatic discovery of potential mirror-miRNAs, and analyzes the frequency of various types of post-transcriptional modifications at each genomic location. Each step of the Prost! analysis are provided into the excel file output for the user to have all information in hands for deeper analysis of specific cases. | / |
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Homepage Publication March 8, 2019 Citations: 21 | ||
| 10 | 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. | / |
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Homepage Publication | ||
| 11 | SeqBuster | A command-line bioinformatic tool usefull for the analysis of deep sequencing data, namely known miRNAs and isomiRs annotation. | / |
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Homepage Publication Dec. 11, 2009 Citations: 108 | ||
| 12 | 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. | / |
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Homepage Publication May 27, 2015 Citations: 118 | ||
| 13 | sRNAtools | sRNAtools can be used to identify and functionally annotate diverse kinds of sncRNA for up to 21 model species (including human, mouse, Arabidopsis, rice, etc.), including (i) profiling of miRNAs, Piwi-interacting RNA (piRNAs), piRNA-producing loci (piRNA cluster), tRNAs, natsiRNA, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs) and rRNAs and (ii) discovering isomiRs, novel miRNAs, tRFs, plant-specific 24-nt siRNAs and phasiRNAs. sRNAtools also provides web-based approaches to detect sncRNAs in multiple transcriptomes. | / |
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Homepage Publication Jan. 18, 2021 Citations: 21 |
