Gesellschaft für Informatik e.V.

Lecture Notes in Informatics


Datenbanksysteme für Business, Technologie und Web (BTW 2015) - Workshopband P-242, 143-150 (2015).

Gesellschaft für Informatik, Bonn
2015


Copyright © Gesellschaft für Informatik, Bonn

Contents

Genome sequence analysis with monetdb: a case study on ebola virus diversity

Robin Cijvat , Stefan Manegold , Martin Kersten , Gunnar W. Klau , Alexander Schönhuth , Tobias Marschall and Ying Zhang

Abstract


Next-generation sequencing (NGS) technology has led the life sciences into the big data era. Today, sequencing genomes takes little time and cost, but results in terabytes of data to be stored and analysed. Biologists are often exposed to excessively time consuming and error-prone data management and analysis hurdles. In this paper, we propose a database management system (DBMS) based approach to accelerate and substantially simplify genome sequence analysis. We have extended MonetDB, an open-source column-based DBMS, with a BAM module, which enables easy, flexible, and rapid management and analysis of sequence alignment data stored as Sequence Alignment/Map (SAM/BAM) files. We describe the main features of MonetDB/BAM using a case study on Ebola virus genomes.


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Gesellschaft für Informatik, Bonn
ISBN 978-3-88579-636-7


Last changed 30.04.2015 15:50:14