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


BACKGROUND
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.
Bartels
Daniela
D
Universität Bielefeld, Center for Biotechnology (CeBiTec) D-33594 Bielefeld, Germany.
Kespohl
Sebastian
S
Albaum
Stefan
S
Drüke
Tanja
T
Goesmann
Alexander
A
Herold
Julia
J
Kaiser
Olaf
O
Pühler
Alfred
A
Pfeiffer
Friedhelm
F
Raddatz
Günter
G
Stoye
Jens
J
Meyer
Folker
F
Schuster
Stephan C
SC
D000465:Algorithms; D001483:Base Sequence; D019985:Benchmarking / Q000379:methods; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface