ShortStack is a stand-alone application that analyzes reference-aligned small RNA-seq data and performs comprehensive de novo annotation and quantification of the inferred small RNA genes. ShortStack's output reports multiple parameters of direct relevance to small RNA gene annotation, including RNA size distributions, repetitiveness, strandedness, hairpin-association, MIRNA annotation, and phasing.

mirTools is a integrated tool to investigate ncRNA sequences, expression levels, differentially expressed ncRNAs and miRNA-targeted genes and their functional annotation, which will be valuable for deciphering the functional roles of ncRNAs hidden in the large amount of NGS data.

CPSS (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.

miRDeep and its varieties are widely used to quantify known and novel micro RNA (miRNA) from small RNA sequencing (RNAseq).

miREval 2.0 is an online tool that can simultaneously search up to 100 sequences for novel microRNAs (miRNAs) in multiple organisms. miREval 2.0 uses multiple published in silico approaches to detect miRNAs in sequences of interest. This tool can be used to discover miRNAs from DNA sequences or to validate candidates from sequencing data.

miRNAkey is a software package designed to be used as a base-station for the analysis of miRNA deep sequencing data. The package implements common steps taken in the analysis of such data, as well as adds unique features, such as data statistics and multiple read determination, generating a novel platform for the analysis of miRNA expression.

miRanalyzer is a web server and stand-alone tool for the detection of known and prediction of new microRNAs in high-throughput sequencing experiments. The new version has been notably improved regarding speed, scope and available features.

MiRTRAP is a computational method for the systematic identification of miRNAs from high throughput sequencing data.

DSAP is 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.

CAP-miRSeq is a comprehensive Analysis Pipeline for microRNA Sequencing data that integrates read pre-processing, alignment, mature/precursor/novel miRNA detection and quantification, data visualization, variant detection in miRNA coding region, and more flexible differential expression analysis between experimental conditions.

miRspring is a software solution that creates a small portable research document that visualizes, calculates and reports on the complexities of miRNA processing.

tRF2Cancer is a web server for identifying tRFs (tRNA-derived small RNA Fragments) and their expression in cancers from small RNA deep-sequencing data.

tDRmapper is a tool for mapping, naming, and quantifying tRNA-derived RNAs (tDRs). tDRmapper was designed specifically for human small RNA-seq data (single-end, 50x) generated on the Illumina sequencing platform using cDNA libraries that were prepared using the Illumina TruSeq protocol. It not only provides a standardized nomenclature and quantification scheme, but also includes graphical visualization that facilitates the discovery of novel transfer RNAs and tRNA-derived RNA biology.

DARIO is a free web service that allows to study short read data from small RNA-seq experiments. It provides a wide range of analysis features, including quality control, read normalization, ncRNA quantification and prediction of putative ncRNA candidates.

DeAnnIso is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data.

PhaseTank is a stand-alone package for systematically characterizing phasiRNAs and their regulatory networks.

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.

miRge 2.0 is comprehensive tool with functionalities including a novel miRNA detection method, A-to-I editing analysis, integrated standardized GFF3 isomiR reporting, and improved alignment to miRNAs.

miRquant 2.0 is an expanded bioinformatics tool for accurate annotation and quantification of microRNAs and their isoforms (termed isomiRs) from small RNA-sequencing data.

unitas is an out-of-the-box ready software for complete annotation of small RNA sequence datasets, supporting the wide range of species for which non-coding RNA reference sequences are available in the Ensembl databases

sRNAnalyzer is a comprehensive and customizable sRNA-Seq data analysis pipeline, which enables: (i) comprehensive miRNA profiling strategies to better handle isomiRs and summarization based on each nucleotide position to detect potential SNPs in miRNAs, (ii) different sequence mapping result assignment approaches to simulate results from microarray/qRT-PCR platforms and a local probabilistic model to assign mapping results to the most-likely IDs, (iii) comprehensive ribosomal RNA filtering for accurate mapping of exogenous RNAs and summarization based on taxonomy annotation

sRNAtoolbox is a collection of several tools for RNA analysis, which 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.

Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data and best practice step-by-step guidelines on how to analyze sRNA-seq data.

The UEA sRNA workbench is a simple to use, downloadable sRNA software package based on algorithms developed in the Computational Biology Laboratory at the University of East Anglia (UEA) 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.

SPAR (Small RNA-seq Portal for Analysis of sequencing expeRiments) is a user-friendly web server for interactive processing, analysis, annotation and visualization of small RNA sequencing data.

The DASHR (Database of small human non-coding RNAs) database provides the most comprehensive information to date on human small non-coding RNA (sncRNA) genes, precursor and mature sncRNA annotations, sequence, expression levels and RNA processing information across 42 normal tissues and cell types in human. The content of the database derives from integrating annotation data with curation, annotation, and computational analysis of 187 small-RNA (smRNA-seq) deep sequencing datasets with over 2.5 billion reads from over 30 independent studies. DASHR contains information on over 48,000 precursor and mature sncRNA annotations in the human genome, of which 82% are expressed in one or more of the curated tissues and cell types.

DASHR V2.0 is a database developed at the University of Pennsylvania with the most comprehensive expression and processing information to date on all major classes of human small non-coding RNA (sncRNA) genes and mature sncNA annotations, expression levels, sequence and RNA processing information across 185 human tissues, cell types, and cell lines. The content of the database derives from integrating annotation data with curation, annotation, and computational analysis of 802 small-RNA (smRNA-seq) deep sequencing datasets with over 22 billion reads from >60 independent studies.

ICE followed by NGS identifies adenosine-to-inosine editing. In this method, RNA is treated with acrylonitrile, while control RNA is untreated. Control and treated RNAs are reverse-transcribed and PCR-amplified. Inosines in RNA fragments treated with acrylonitrile cannot be reverse-transcribed. Deep sequencing of the cDNA prepared from control and treated RNA provides high-resolution reads of inosines in RNA fragments.

MeRIP-Seq (Methylated RNA Immunoprecipitation Sequencing) maps methylated RNA. In this method, modification-specific antibodies are used to immunoprecipitate RNA. RNA is reverse-transcribed to cDNA and sequenced. Deep sequencing provides high-resolution reads of methylated RNA.

miCLIP-m6A (m6A Individual-Nucleotide-Resolution Crosslinking and Immunoprecipitation) maps m6A locations in the transcriptome with single-nucleotide resolution. In this method, anti-m6A antibodies are crosslinked to mRNA sequences, and a cDNA library is prepared and sequenced. The cDNA library preparation in miCLIP follows the iCLIP protocol closely.

PA-m6A-seq is a photo-crosslinking-assisted m6A sequencing strategy to more accurately define sites with m6A modification.

m6A-LAIC-seq (m6A-level and isoform-characterization sequencing) is a method to quantify transcript copies of particular genes with m6A modified ('m6A levels') or the relationship of m6A modification(s) to alternative RNA isoforms.

Bisulfite-seq can be used to map modified cytosine sites across a human transcriptome

m5C-RIP (m5C RNA immunoprecipitation)

Aza-IP (5-azacytidine–mediated RNA immunoprecipitation) exploits the catalytic mechanisms of the m5C methyltransferases to covalently link methyltransferase to its RNA targets. First, the cytidine analog 5-azacytidine is randomly incorporated into the nascent RNA of cells overexpressing an epitope-tagged m5C RNA methyltransferase. Due to the nitrogen substitution at the C5 position, a stable covalent bond forms when the RNA methyltransferase attacks the C6 position of its RNA targets. These targets are enriched by immunoprecipitation and subsequently sequenced.

Ψ-seq is a method to transcriptome-wide quantitative mapping of Ψ, which has been used to identify the vast majority of Ψ sites in rRNA, tRNA and snRNA and dozens of novel sites within snoRNAs and mRNAs.

CeU-Seq (N3-CMC-enriched pseudouridine sequencing) is a selective chemical labeling and pulldown method, which identified 2,084 Ψ sites within 1,929 human transcripts.

Pseudo-Seq detects pseudouridylation sites in ncRNAs with single-nucleotide resolution using high-throughput sequencing. Pseudo-Seq is very similar to PSI-seq, in that both methods use CMC to modify pseudouridines selectively and halt reverse transcription. However, Pseudo-Seq circularizes cDNA strands before PCR amplification and purification, instead of using ARTseq.

PSI-Seq (Pseudouridine Site Identification Sequencing) identifies RNA sequences containing pseudouridine sites using high-throughput sequencing. PSI-Seq uses N-Cyclohexyl-N_-(2-morpholinoethyl)carbodiimide (CMC) to modify pseudouridines selectively, effectively halting reverse transcription. The cDNA libraries are prepared by the ARTseq method.

m1A-seq is based on methylated RNA immunoprecipitation sequencing (MeRIP-seq), which is used for transcriptome-wide localization of m1A sites and coupled it to an orthogonal chemical method based on Dimroth rearrangement to obtain high-resolution m1A maps

m1A-ID-seq technique is based on m1A immunoprecipitation and the inherent ability of m1A to stall reverse transcription, as a means for transcriptome-wide m1A profiling.

TRAC-seq is m7G methylated tRNA immunoprecipitation sequencing (MeRIP-seq) and tRNA reduction and cleavage sequencing to reveal the m7G tRNA methylome

AlkAniline-Seq is a new principle of RNAseq library preparation, which relies on a chemistry based positive enrichment of reads in the resulting libraries, and therefore leads to unprecedented signal-to-noise ratios. It enables a deep sequencing-based technology for the simultaneous detection of 7-methylguanosine (m7G) and 3-methylcytidine (m3C) in RNA at single nucleotide resolution.