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

Kaiser O, Bartels D, Bekel T, Goesmann A, Kespohl S, Pühler A, Meyer F (2003)
JOURNAL OF BIOTECHNOLOGY 106(2-3): 121-133.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
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. (C) 2003 Elsevier B.V. All rights reserved.
Erscheinungsjahr
Zeitschriftentitel
JOURNAL OF BIOTECHNOLOGY
Band
106
Zeitschriftennummer
2-3
Seite
121-133
ISSN
PUB-ID

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Kaiser O, Bartels D, Bekel T, et al. Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY. 2003;106(2-3):121-133.
Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A., & Meyer, F. (2003). Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY, 106(2-3), 121-133. doi:10.1016/j.jbiotec.2003.08.008
Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A., and Meyer, F. (2003). Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY 106, 121-133.
Kaiser, O., et al., 2003. Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY, 106(2-3), p 121-133.
O. Kaiser, et al., “Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique”, JOURNAL OF BIOTECHNOLOGY, vol. 106, 2003, pp. 121-133.
Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A., Meyer, F.: Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique. JOURNAL OF BIOTECHNOLOGY. 106, 121-133 (2003).
Kaiser, O., Bartels, D., Bekel, Thomas, Goesmann, Alexander, Kespohl, S., Pühler, Alfred, and Meyer, F. “Whole genome shotgun sequencing guided-by bioinformatics pipelines - An optimized approach for an established technique”. JOURNAL OF BIOTECHNOLOGY 106.2-3 (2003): 121-133.

14 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Whole-genome sequencing and gene mapping of a newly isolated lytic enterococcal bacteriophage EFRM31.
Fard RM, Barton MD, Arthur JL, Heuzenroeder MW., Arch Virol 155(11), 2010
PMID: 20844906
The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A., J Biotechnol 140(1-2), 2009
PMID: 19297685
The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity.
Gartemann KH, Abt B, Bekel T, Burger A, Engemann J, Flügel M, Gaigalat L, Goesmann A, Gräfen I, Kalinowski J, Kaup O, Kirchner O, Krause L, Linke B, McHardy A, Meyer F, Pohle S, Rückert C, Schneiker S, Zellermann EM, Pühler A, Eichenlaub R, Kaiser O, Bartels D., J Bacteriol 190(6), 2008
PMID: 18192381
The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
Vorhölter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Rückert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Pühler A., J Biotechnol 134(1-2), 2008
PMID: 18304669
Complete genome sequence of the myxobacterium Sorangium cellulosum.
Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Muñoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Rückert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorhölter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blöcker H, Pühler A, Müller R., Nat Biotechnol 25(11), 2007
PMID: 17965706
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis.
Schneiker S, Martins dos Santos VA, Bartels D, Bekel T, Brecht M, Buhrmester J, Chernikova TN, Denaro R, Ferrer M, Gertler C, Goesmann A, Golyshina OV, Kaminski F, Khachane AN, Lang S, Linke B, McHardy AC, Meyer F, Nechitaylo T, Pühler A, Regenhardt D, Rupp O, Sabirova JS, Selbitschka W, Yakimov MM, Timmis KN, Vorhölter FJ, Weidner S, Kaiser O, Golyshin PN., Nat Biotechnol 24(8), 2006
PMID: 16878126
The crystal structure of hypothetical methyltransferase from Thermus thermophilus HB8.
Sasaki C, Sugiura I, Ebihara A, Tamura T, Sugio S, Inagaki K., Proteins 64(2), 2006
PMID: 16700050
Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.
Krause A, Ramakumar A, Bartels D, Battistoni F, Bekel T, Boch J, Böhm M, Friedrich F, Hurek T, Krause L, Linke B, McHardy AC, Sarkar A, Schneiker S, Syed AA, Thauer R, Vorhölter FJ, Weidner S, Pühler A, Reinhold-Hurek B, Kaiser O, Goesmann A., Nat Biotechnol 24(11), 2006
PMID: 17057704
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
Bartels D, Kespohl S, Albaum S, Drüke T, Goesmann A, Herold J, Kaiser O, Pühler A, Pfeiffer F, Raddatz G, Stoye J, Meyer F, Schuster SC., Bioinformatics 21(7), 2005
PMID: 15514001
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Pühler A., J Bacteriol 187(13), 2005
PMID: 15968079
Shotgun sequencing of the negative-sense RNA genome of the rhabdovirus Maize mosaic virus.
Reed SE, Tsai CW, Willie KJ, Redinbaugh MG, Hogenhout SA., J Virol Methods 129(1), 2005
PMID: 16005085
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.
Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O., J Bacteriol 187(21), 2005
PMID: 16237009

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