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.

sRNATarBase database, which was initially developed in 2010. The new version (recently moved to http://ccb1.bmi.ac.cn/srnatarbase/) contains 771 sRNA-target entries manually collected from 213 papers, and 23 290 and 11 750 predicted targets from sRNATarget and sTarPicker, respectively. Among the 771 entries, 475 and 17 were involved in validated sRNA-mRNA and sRNA-protein interactions, respectively, while 279 had no reported interactions.

Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: for the human genome, the index is typically about 2.2 GB (for unpaired alignment) or 2.9 GB (for paired-end alignment). Multiple processors can be used simultaneously to achieve greater alignment speed. Bowtie can also output alignments in the standard SAM format, allowing Bowtie to interoperate with other tools supporting SAM, including the SAMtools consensus, SNP, and indel callers. Bowtie runs on the command line under Windows, Mac OS X, Linux, and Solaris.

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the 3’ sequencing adapter because the read is longer than the molecule that is sequenced. Amplicon reads start with a primer sequence. Poly-A tails are useful for pulling out RNA from your sample, but often you don’t want them to be in your reads.Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter single-end and paired-end reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Cutadapt can also demultiplex your reads.

sRNAdb allows a user-friendly and comprehensive comparative analysis of sRNAs from available sequenced gram-positive prokaryotic replicons. Offline versions including analysis and visualization tools facilitate complex user specific bioinformatics analyses.

The sRNAanno database hosts a large collection of miRNA, phasiRNA- and hc-siRNA-generating loci annotated from ~140 plants using consistent and high-confident criteria. All the annotations are made freely available to the scientific community via various services and tools.

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.Next-Generation sequencing machines usually produce FASTA or FASTQ files, containing multiple short-reads sequences (possibly with quality information).The main processing of such FASTA/FASTQ files is mapping (aka aligning)the sequences to reference genomes or other databases using specialized programs.

miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs.

MIREAP combines small RNA position and depth with a model of microRNA biogenesis to discover microRNAs from deeply sequenced small RNA libraries.

RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

Target predictions are based on a development of the miRanda algorithm which incorporates current biological knowledge on target rules and on the use of an up-to-date compendium of mammalian microRNAs.

TargetFinder will computationally predict small RNA binding sites on target transcripts from a sequence database. This is done by aligning the input small RNA sequence against all transcripts, followed by site scoring using a position-weighted scoring matrix.

tapir is a software for the prediction of plant microRNA targets.TAPIR is using the software RNAhybrid developped by Marc Rehmsmeier for the sensitive search option (see http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/).

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.