Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets
Java R
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exceRpt small-RNAseq pipeline

Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets.


Rob Kitchen,


exceRpt_smallRNA -- This choreographs the processing, filtering, and alignment of a single smallRNA-seq sample. The script is a makefile and

mergePipelineRuns.R -- This script will take as input a directory containing 1 or more subdirectories or zipfiles containing output from the pipeline above. In this way, results from 1 or more smallRNA-seq samples can be combined, several QC plots are generated, and the read-counts are normalised ready for downstream analysis by clustering and/or differential expression.

Please see the exceRpt mainpage ( for instructions as to how to use the software


exceRpt_smallRNA -- requires numerous dependences that require some familiarity with UNIX. The software is installed on the Genboree Workbench ( which provides a graphical interface to the pipeline that is free for academic use. Alternatively, development of a Docker image ( for this software is available, if you are interested in this please feel free browse the documentation ( or get in touch using the email address above.

mergePipelineRuns.R -- is comparatively much simpler to install. Once the R software ( is set up on your system the script should automatically identify and install all required dependencies. Again, this script is available on the Genboree Workbench ( and is also free for academic use.