BACCardl - A tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

Daniela Bartels; Sebastian Kespohl; Stefan Albaum; Tanja Drüke; Alexander Goesmann; Julia Herold; Olaf Kaiser; Alfred Pühler; Friedhelm Pfeiffer; Günter Raddatz; Jens Stoye; Folker Meyer; Stephan C. Schuster

doi:10.1093/bioinformatics/bti091

BACCardl - A tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

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

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

31 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	853-859
Number of pages	7
Journal	Bioinformatics
Volume	21
Issue number	7
DOIs	https://doi.org/10.1093/bioinformatics/bti091
Publication status	Published - Apr 1 2005
Externally published	Yes

ASJC Scopus Subject Areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/bti091

Cite this

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abstract = "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.",

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AU - Bartels, Daniela

AU - Kespohl, Sebastian

AU - Albaum, Stefan

AU - Drüke, Tanja

AU - Goesmann, Alexander

AU - Herold, Julia

AU - Kaiser, Olaf

AU - Pühler, Alfred

AU - Pfeiffer, Friedhelm

AU - Raddatz, Günter

AU - Stoye, Jens

AU - Meyer, Folker

AU - Schuster, Stephan C.

PY - 2005/4/1

Y1 - 2005/4/1

N2 - 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.

AB - 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.

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BACCardl - A tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison

Abstract

ASJC Scopus Subject Areas

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