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2015 ; 1
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SMiRK: an Automated Pipeline for miRNA Analysis
#MMPMID26613105
Milholland B
; Gombar S
; Suh Y
Source J Genom
2015[Jun]; 1
(1
): ä PMID26613105
show ga
BACKGROUND: Micro RNAs (miRNAs), important regulators of cell function, can be
interrogated by high-throughput sequencing in a rapid and cost-effective manner.
However, the tremendous amount of data generated by such methods is not easily
analyzed. In order to extract meaningful information and draw biological
conclusions from miRNA data, many challenges in quality control, alignment,
normalization, and analysis must be overcome. Typically, these would only be
possible with the dedicated efforts of a specialized computational biologist for
a sustained period of time. RESULTS: Here, we present SMiRK, an automated
pipeline that allows such tasks to be completed with minimal time and without
dedicated bioinformatics personnel. SMiRK's flexibility also allows experienced
users to exert more control, if they wish. We describe how SMiRK automatically
normalizes the data, removes low-information miRNAs, and produces heatmaps of the
processed data. We give details on SMiRK's implementation and use cases for
novice and advanced users. As a demonstration of its capabilities, SMiRK was used
to rapidly and automatically analyze a dataset taken from the literature.
CONCLUSION: SMiRK is a useful and efficient tool that can be used by
investigators at multiple skill levels. Those who lack bioinformatics training
can use it to easily and automatically analyze their data, while those with
experience will find it beneficial to not need to write tools from scratch.
free
free
free
