Barnacle: an assembly algorithm for clone-based sequences of whole genomes.

We propose an assembly algorithm Barnacle for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we show, Barnacle more effectively resolves conflicts due to repeated sequences which is the main difficulty of the sequence assembly problem. In addition, we are able to detect inconsistencies in the underlying data. We present and compare our results on the December 2001 freeze of the public working draft of the human genome with NCBI's assembly (Build 28). The assembly of December 2001 freeze of the public working draft generated by Barnacle and the source code of Barnacle are available at (http://www.cs.rutgers.edu/~vchoi).