  We propose an assembly algorithm {\sc 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, {\sc Barnacle} more effectively resolves conflicts due
to repeated sequences. The latter is the main difficulty of the sequence
assembly problem. Inaddition, 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
{\sc Barnacle} and the source code of {\sc Barnacle} are available at
(http://www.cs.rutgers.edu/~vchoi).
