NDLI: SMITH: a LIMS for handling next-generation sequencing workflows

Please wait, while we are loading the content...

SMITH: a LIMS for handling next-generation sequencing workflows

Content Provider	Springer Nature : BioMed Central
Author	Venco, Francesco Vaskin, Yuriy Ceol, Arnaud Muller, Heiko
Abstract	Background Life-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). Methods SMITH 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. Results 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. Conclusions SMITH standardizes, automates, and speeds up sequencing workflows. Annotation of data with key-value pairs facilitates meta-analysis.
Related Links	https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-S14-S3.pdf
Ending Page	8
Page Count	8
Starting Page	1
File Format	HTM / HTML
ISSN	14712105
DOI	10.1186/1471-2105-15-S14-S3
Journal	BMC Bioinformatics
Issue Number	14
Volume Number	15
Language	English
Publisher	BioMed Central
Publisher Date	2014-11-27
Access Restriction	Open
Subject Keyword	Bioinformatics Microarrays Computational Biology Computer Appl. in Life Sciences Algorithms Next Generation Sequencing Information Management System FASTQ File Next Generation Sequencing Data Sequencing Request Computational Biology/Bioinformatics
Content Type	Text
Resource Type	Article
Subject	Molecular Biology Biochemistry Computer Science Applications Applied Mathematics Structural Biology
Journal Impact Factor	2.9/2023
5-Year Journal Impact Factor	3.6/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

SMITH: a LIMS for handling next-generation sequencing workflows.

Light-weight reference-based compression of FASTQ data

SRAdb: query and use public next-generation sequencing data from within R

ANGSD: Analysis of Next Generation Sequencing Data

SMITH: a LIMS for handling next-generation sequencing workflows

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files

HPG pore: an efficient and scalable framework for nanopore sequencing data

MPD: multiplex primer design for next-generation targeted sequencing

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data

SMITH: a LIMS for handling next-generation sequencing workflows

Similar Documents

SMITH: a LIMS for handling next-generation sequencing workflows.

Light-weight reference-based compression of FASTQ data

SRAdb: query and use public next-generation sequencing data from within R

ANGSD: Analysis of Next Generation Sequencing Data

SMITH: a LIMS for handling next-generation sequencing workflows

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files

HPG pore: an efficient and scalable framework for nanopore sequencing data

MPD: multiplex primer design for next-generation targeted sequencing

SeqAssist: a novel toolkit for preliminary analysis of next-generation sequencing data

SMITH: a LIMS for handling next-generation sequencing workflows