title: Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique.
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.
authors.affiliation: Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany. olaf.kaiser@genetik.uni-bielefeld.de
authors.forename: Olaf
authors.initials: O
authors.lastname: Kaiser
authors.forename: Daniela
authors.initials: D
authors.lastname: Bartels
authors.forename: Thomas
authors.initials: T
authors.lastname: Bekel
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.forename: Sebastian
authors.initials: S
authors.lastname: Kespohl
authors.forename: Alfred
authors.initials: A
authors.lastname: Pühler
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
mesh_terms: 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
chemical_list: D004269:DNA, Bacterial