Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique.
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.
Kaiser
Olaf
O
Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany. olaf.kaiser@genetik.uni-bielefeld.de
Bartels
Daniela
D
Bekel
Thomas
T
Goesmann
Alexander
A
Kespohl
Sebastian
S
Pühler
Alfred
A
Meyer
Folker
F
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D004269:DNA, Bacterial / Q000235:genetics*; D003628:Database Management Systems; D020869:Gene Expression Profiling / Q000379:methods*; D016680:Genome, Bacterial; D011786:Quality Control; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D004269:DNA, Bacterial