An algorithm for automated closure during assembly.

ABSTRACT:

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 bou

SUBMITTER: Koren S 

PROVIDER: S-EPMC2945939 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature