SMITH: a LIMS for handling next-generation sequencing workflows

BMC Bioinformatics

Research

Heiko Muller¹  Arnaud Ceol¹  Francesco Venco²  Yuriy Vaskin² 

[1] Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT), 20139, Milan, Italy;Department of Electronics, Information and Bioengineering, Politecnico of Milan, 20133, Milan, Italy;

关键词: Next Generation Sequencing;    Information Management System;    FASTQ File;    Next Generation Sequencing Data;    Sequencing Request;   

DOI  :  10.1186/1471-2105-15-S14-S3

来源: Springer

【 摘 要 】

BackgroundLife-science laboratories make increasing use of Next Generation Sequencing (NGS) for studying bio-macromolecules and their interactions. Array-based methods for measuring gene expression or protein-DNA interactions are being replaced by RNA-Seq and ChIP-Seq. Sequencing is generally performed by specialized facilities that have to keep track of sequencing requests, trace samples, ensure quality and make data available according to predefined privileges.An integrated tool helps to troubleshoot problems, to maintain a high quality standard, to reduce time and costs. Commercial and non-commercial tools called LIMS (Laboratory Information Management Systems) are available for this purpose. However, they often come at prohibitive cost and/or lack the flexibility and scalability needed to adjust seamlessly to the frequently changing protocols employed.In order to manage the flow of sequencing data produced at the Genomic Unit of the Italian Institute of Technology (IIT), we developed SMITH (Sequencing Machine Information Tracking and Handling).MethodsSMITH is a web application with a MySQL server at the backend. 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. 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.ResultsSMITH 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.ConclusionsSMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis.

【 授权许可】

Unknown   
© Venco et al.; licensee BioMed Central. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.