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.
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.
Authors: Frank Thieme; Ralf Koebnik; Thomas Bekel; Carolin Berger; Jens Boch; Daniela Büttner; Camila Caldana; Lars Gaigalat; Alexander Goesmann; Sabine Kay; Oliver Kirchner; Christa Lanz; Burkhard Linke; Alice C McHardy; Folker Meyer; Gerhard Mittenhuber; Dietrich H Nies; Ulla Niesbach-Klösgen; Thomas Patschkowski; Christian Rückert; Oliver Rupp; Susanne Schneiker; Stephan C Schuster; Frank-Jörg Vorhölter; Ernst Weber; Alfred Pühler; Ulla Bonas; Daniela Bartels; Olaf Kaiser Journal: J Bacteriol Date: 2005-11 Impact factor: 3.490
Authors: Eva Trost; Susanne Götker; Jessica Schneider; Susanne Schneiker-Bekel; Rafael Szczepanowski; Alexandra Tilker; Prisca Viehoever; Walter Arnold; Thomas Bekel; Jochen Blom; Karl-Heinz Gartemann; Burkhard Linke; Alexander Goesmann; Alfred Pühler; Sanjay K Shukla; Andreas Tauch Journal: BMC Genomics Date: 2010-02-05 Impact factor: 3.969
Authors: Patrick C Y Woo; Susanna K P Lau; Herman Tse; Jade L L Teng; Shirly O T Curreem; Alan K L Tsang; Rachel Y Y Fan; Gilman K M Wong; Yi Huang; Nicholas J Loman; Lori A S Snyder; James J Cai; Jian-Dong Huang; William Mak; Mark J Pallen; Si Lok; Kwok-Yung Yuen Journal: PLoS Genet Date: 2009-03-13 Impact factor: 5.917