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Bioinformatics Advance Access originally published online on October 28, 2004
Bioinformatics 2005 21(7):853-859; doi:10.1093/bioinformatics/bti091
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Published by Oxford University Press 2004.

BACCardI—a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

Daniela Bartels 1, Sebastian Kespohl 1, Stefan Albaum 1, Tanja Drüke 1, Alexander Goesmann 1, Julia Herold 1, Olaf Kaiser 2, Alfred Pühler 2, Friedhelm Pfeiffer 3, Günter Raddatz 4, Jens Stoye 5, Folker Meyer 1,* and Stephan C. Schuster 4,*

1Universität Bielefeld, Center for Biotechnology (CeBiTec) D-33594 Bielefeld, Germany
2Universität Bielefeld, Lehrstuhl für Genetik, Fakultät für Biologie D-33594 Bielefeld, Germany
3Max-Planck-Institut für Biochemie, Abt. Membranbiochemie Am Klopferspitz 18a, D-82152 Martinsried, Germany
4Max-Planck-Institut für Entwicklungsbiologie Spemannstr. 35, D-72076 Tübingen, Germany
5Universität Bielefeld, Technische Fakultät D-33594 Bielefeld, Germany

*To whom correspondence should be addressed.

Summary: We provide the graphical tool BACCardI for the construction of virtual clone maps from standard assembler output files or BLAST based sequence comparisons. This new tool has been applied to numerous genome projects to solve various problems including (a) validation of whole genome shotgun assemblies, (b) support for contig ordering in the finishing phase of a genome project, and (c) intergenome comparison between related strains when only one of the strains has been sequenced and a large insert library is available for the other. The BACCardI software can seamlessly interact with various sequence assembly packages.

Motivation: Genomic assemblies generated from sequence information need to be validated by independent methods such as physical maps. The time-consuming task of building physical maps can be circumvented by virtual clone maps derived from read pair information of large insert libraries.

Availability: The BACCardI tool is freely available at http://www.cebitec.uni-bielefeld.de/groups/brf/software/baccardi/

Contact: fm{at}Cebitec.Uni-Bielefeld.DE


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