Sciweavers

Share
BMCBI
2010

An algorithm for automated closure during assembly

10 years 2 months ago
An algorithm for automated closure during assembly
Background: Finishing is the process of improving the quality and utility of draft genome sequences generated by shotgun sequencing and computational assembly. Finishing can involve targeted sequencing. Finishing reads may be incorporated by manual or automated means. One automated method uses targeted addition by local re-assembly of gap regions. An obvious alternative uses de novo assembly of all the reads. Results: A procedure called the bounding read algorithm was developed for assembly of shotgun reads plus finishing reads and their constraints, targeting repeat regions. The algorithm was implemented within the Celera Assembler software and its pyrosequencing-specific variant, CABOG. The implementation was tested on Sanger and pyrosequencing data from six genomes. The bounding read assemblies were compared to assemblies from two other methods on the same data. The algorithm generates improved assemblies of repeat regions, closing and tiling some gaps while degrading none. Conclus...
Sergey Koren, Jason R. Miller, Brian Walenz, Grang
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Sergey Koren, Jason R. Miller, Brian Walenz, Granger G. Sutton
Comments (0)
books