SMITH – a LIMS for handling next-generation sequencing workflows

Wet-lab scientists of the Centre for Genomic Science and database experts from the Politecnico of Milan in the context of a Genomic Data Model Project developed SMITH a web application with a MySQL server at the backend.  The data base schema stores all the information of an NGS experiment, including the descriptions of all protocols and algorithms used in the process. Notably, an attribute-value table allows associating an unconstrained textual description to each sample and all the data produced afterwards. This method permits the creation of metadata that can be used to search the database for specific files as well as for statistical analyses.

SMITH runs automatically and limits direct human interaction mainly to administrative tasks. SMITH data-delivery procedures were standardized making it easier for biologists and analysts to navigate the data. Automation also helps saving time. The workflows are available through an API provided by the workflow management system. The parameters and input data are passed to the workflow engine that performs de-multiplexing, quality control, alignments, etc.


Availability – The demo version of SMITH is available at The maintained source code is freely available at under the terms of the MIT licence.

Venco F, Vaskin Y, Ceol A, Muller H. (2014) SMITH: a LIMS for handling next-generation sequencing workflows. BMC Bioinformatics 15 Suppl 14:S3. [article]

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