Having produced a complete Happily anchored map of Cryptosporidium parvum, the map of chromosome 6 was used to identify a tiling path across the full length of the chromosome.

Unlike conventional approaches, gap closure could be carried out concurrently with sequencing. Potential mis-assemblies were avoided since all markers in the map had already been positioned and oriented with respect to each other.

We found that large insert clones of cryptosporidium had a tendency to be unstable. The map proved invaluable in identifying situations where segments of insert had been spontaneously deleted.

Even after exhaustive screening of the libraries, however, two clone gaps remained. Isolation of a genomic fragment spanning both gaps, followed by shotgun sequencing, also failed to close the sequence gaps suggesting that these sequences were particularly difficult to maintain in bacterial clones.

The selected clones, mostly PACs but also a few BACs, covering the bulk were shotgun sequenced and aligned with each other to produce an entire chromosome sequence Genome Res. 13:1787-1799, 2003