miRPursuit – a pipeline for automated analyses of small RNAs in model and nonmodel plants

Researchers from the Institute of Experimental Biology and Technology, Portugal introduce miRPursuit, a pipeline developed for running end-to-end analyses of high-throughput small RNA (sRNA) sequence data in model and nonmodel plants, from raw data to identified and annotated conserved and novel sequences. It consists of a series of UNIX shell scripts, which connect open-source sRNA analysis software. The involved parameters can be combined with convenient workflow management by users without advanced computational skills. miRPursuit presents several advantages when compared to other tools, including the possibility of processing several sRNA libraries in parallel, thus easily allowing a comparison of the differences in sRNA read accumulation among sRNA libraries. The developers validate miRPursuit by using datasets from a model plant and discuss its performance with the analysis of sRNAs from non-model species.

miRPursuit pipeline diagram and miRPursuit file structure

rna-seq

Each rectangle represents a folder, dotted lines indicate relative paths, while solid lines indicate folder is child of arrow origin. /miRPursuit is located in the path where it was installed. /[workdir_name] has the path that was set in workdir in workdir.cfg. /config has all the configuration files specified in Appendix S1. /count has all count files generated. /data stores all generated files along if any intermediary files generated by the processes in the pipeline. /log stores all the log file related to the pipeline execution.

Chaves I, Costa BV, Rodrigues AS, Bohn A, Miguel CM. (2017) miRPursuit-a pipeline for automated analyses of small RNAs in model and nonmodel plants. FEBS Lett 591(15):2261-2268. [abstract]

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