What is miARmaSeq?

Introduction:

miARma-Seq, which stands for miRNA-Seq And RNA-Seq Multiprocess Analysis, is a suite designed to study mRNAs, miRNAs and circRNAs. It is able to perform differential expression analysis, miRNA-mRNA target prediction and functional analysis among others. Most importantly, it can be applied to any sequenced organism, and it can be initiated at any step of the workflow.
As a stand-alone tool, is both easy to install and extremely flexible in terms of its use. It brings together well-established software in a single bundle, allowing a complete analysis from raw data. All the capabilities can be easily and simultaneously enabled at will, regardless the step in the workflow.
Source code is freely distributed. Stable versions can be downloaded from this link and development versions from this other link.

Main Features: 

  • Integrated capabilities that enable data from both miRNA and mRNA expression experiments to be analyzed simultaneously.

  • No restrictions regarding the reference organism as it can be used with any reference organism as long as its genome has been sequenced.

  • Flexibility in terms of fitting any experimental design, allowing the user to start the analysis at different steps of the pipeline.

  • Speed of execution, allowing the pipeline to be executed in a standard computer or in a cluster environment (profiting from its parallelizing properties)

  • Reliability, as the tool performs the analysis with the most of the high-quality standard tools available.

  • Wide coverage, which not only includes miRNA-Seq and RNA-Seq data analysis to identify miRNAs, mRNAs or circRNAs but also, the possibility to carry out :

    • Differential expression analyses for:

      • miRNAs

      • mRNAs

      • circRNAs

  • circRNA identification and quantification.

  • Functional analyses (KEGG and GO terms enrichment).

  • miRNA-mRNA target prediction.

  • miRNA DeNovo Prediction.

  • Easy installation, without having to check otherwise tedious requirements that make the analysis more difficult for non-experienced researchers. miARma aim to avoid tedious installation process by providing a compedium of well-stablished programms for NGS analyis where installation is not needed. All programs listed below are included by default in its latest version:

  • Standard format output files. All output files and results generated with miARmaSeq are in standard formats, like SAM, BAM, PDF, TSV, XLS.