Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique

Olaf Kaiser; Daniela Bartels; Thomas Bekel; Alexander Goesmann; Sebastian Kespohl; Alfred Pühler; Folker Meyer

doi:10.1016/j.jbiotec.2003.08.008

Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique

J Biotechnol. 2003 Dec 19;106(2-3):121-33. doi: 10.1016/j.jbiotec.2003.08.008.

Authors

Olaf Kaiser¹, Daniela Bartels, Thomas Bekel, Alexander Goesmann, Sebastian Kespohl, Alfred Pühler, Folker Meyer

Affiliation

¹ Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany. olaf.kaiser@genetik.uni-bielefeld.de

PMID: 14651855
DOI: 10.1016/j.jbiotec.2003.08.008

Abstract

While the sequencing of bacterial genomes has become a routine procedure at major sequencing centers, there are still a number of genome projects at small- or medium-size facilities. For these facilities a maximum of control over sequencing, assembling and finishing is essential. At the same time, facilities have to be able to co-operate at minimum costs for the overall project. We have established a pipeline for the distributed sequencing of Alcanivorax borkumensis SK2, Azoarcus sp. BH72, Clavibacter michiganensis subsp. michiganensis NCPPB382, Sorangium cellulosum So ce56 and Xanthomonas campestris pv. vesicatoria 85-10. Our pipeline relies on standard tools (e.g. PHRED/PHRAP, CAP3 and Consed/Autofinish) wherever possible, supplementing them with new tools (BioMake and BACCardI) to achieve the aims described above.

Publication types

Comparative Study
Evaluation Study
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Computational Biology / methods
DNA, Bacterial / genetics*
Database Management Systems
Gene Expression Profiling / methods*
Genome, Bacterial*
Quality Control
Sequence Analysis, DNA / methods*
Software*
User-Computer Interface*

Substances

DNA, Bacterial