Related Experiment Video
Updated: Feb 6, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
Published on: March 15, 2019
Processing of big heterogeneous genomic datasets for tertiary analysis of Next Generation Sequencing data
Marco Masseroli1, Arif Canakoglu1, Pietro Pinoli1
1Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy.
Motivation:
We previously proposed a paradigm shift in genomic data management, based on the Genomic Data Model (GDM) for mediating existing data formats and on the GenoMetric Query Language (GMQL) for supporting, at a high level of abstraction, data extraction and the most common data-driven computations required by tertiary data analysis of Next Generation Sequencing datasets. Here, we present a new GMQL-based system with enhanced accessibility, portability, scalability and performance.
Results:
The new system has a well-designed modular architecture featuring: (i) an intermediate representation supporting many different implementations (including Spark, Flink and SciDB); (ii) a high-level technology-independent repository abstraction, supporting different repository technologies (e.g., local file system, Hadoop File System, database or others); (iii) several system interfaces, including a user-friendly Web-based interface, a Web Service interface, and a programmatic interface for Python language. Biological use case examples, using public ENCODE, Roadmap Epigenomics and TCGA datasets, demonstrate the relevance of our work.
Availability And Implementation:
The GMQL system is freely available for non-commercial use as open source project at: http://www.bioinformatics.deib.polimi.it/GMQLsystem/.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
Genomics
Next-generation Sequencing
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Tertiary Healthcare System
Analysis of Population Pharmacokinetic Data
Genomic Imprinting and Inheritance
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
Nomenclature of Secondary and Tertiary Amines

