SMITH: a LIMS for handling next-generation sequencing workflows

Abstract

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.

Data Management for Heterogeneous Genomic Datasets

“…In contrast to other data models and LIMS [30], it clearly divides observations, i.e., genomic regions, from metadata, i.e., available information about how observations are collected. For the former, GDM provides a flat attributebased organization, by imposing that each dataset is associated with a given data schema; the first five attributes of such schema are fixed and represent the sample identity and genomic coordinates.…”

Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions

“…SMITH (Venco et al, 2014) offers a complete automatic system for handling NGS data on high performance computing clusters (HPCs) and can run various downstream workflows through the Galaxy Workflow Management System (WMS) (Blankenberg et al, 2007; Boekel et al, 2015), limiting the user interaction only to administrative tasks. MendeLIMS (Grimes and Ji, 2014) is mainly focused on the management of clinical genome sequencing projects.…”

“…HTS-flow was designed to work together with a LIMS, used for the management of the NGS data from a sequencing facility. In our Research Institute, the samples submitted to sequencing are centrally managed with the SMITH LIMS (Venco et al, 2014), which takes care of keeping track and distributing the raw sequencing data to the specific research group and user. These raw NGS data are automatically visible within HTS-flow for further analysis (Issue 1).…”

Parkour LIMS: facilitating high-quality sample preparation in next generation sequencing

“…Multiple non-commercial open-source solutions exist that offer a wide range of functionality and are applied in laboratories of different scopes and scale. For instance, GNomEx (Nix et al 2010) , openBIS (Barillari et al 2016) and SMITH (Venco et al 2014) provide extensive solutions for sample submission, tracking, billing, data organization and analysis. The data analysis platform Galaxy has a LIMS extension (Scholtalbers et al 2013) for sample tracking, interactive flowcell design and automated sample demultiplexing.…”