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A pipeline designed to analyse RNA sequencing data by producing graphical and MySQL output. Nine different steps of analyses are possible, ranging from trimming to annotation or pattern search. The pipeline output includes graphical summaries, text files that can be easily parsed and automatic construction of a MySQL database, which allows simultaneous querying of expression and annotation data.

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shortran classification

shortran specifications

Software type:
Restrictions to use:
Programming languages:
Perl, Python
Command line interface
Operating system:
Unix/Linux, Mac OS
Computer skills:

shortran distribution


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Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarthus, Denmark; Bioinformatics Research Centre, Aarhus University, Aarthus, Denmark

Funding source(s)

Funded by the Danish National Research Foundation.

Link to literature

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