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Bioinformatics. 2018 Oct 8. doi: 10.1093/bioinformatics/bty843. [Epub ahead of print]

QuagmiR: A Cloud-based Application for IsomiR Big Data Analytics.

Author information

1
RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick,MD.
2
Seven Bridges Genomics Inc., Cambridge, MA.

Abstract

Summary:

MicroRNAs (miRNAs) function as master regulators of gene expression. Recent studies demonstrate that miRNA isoforms (isomiRs) play a unique role during cancer development. Here, we present QuagmiR, the first cloud-based tool to analyze isomiRs from next generation sequencing data. Using a novel and flexible searching algorithm designed for the detection and annotation of heterogeneous isomiRs, it permits extensive customization of the query process and reference databases to meet the user's diverse research needs.

Availability and implementation:

QuagmiR is written in Python and can be obtained freely from GitHub (https://github.com/Gu-Lab-RBL-NCI/QuagmiR). QuagmiR can be run from the command line on local machines, as well as on 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 (https://cancergenomicscloud.org).

Supplementary information:

Supplementary data are available at Bioinformatics online.

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