Primary assembly: a complete assembly with long stretches of phased blocks. The concept has been used by GRC. BAC-to-BAC assemblies can all be regarded as primary assemblies. Falcon-unzip is perhaps the first to produce such assemblies for whole-genome shotgun data.
Alternate assembly: an incomplete assembly consisting of haplotigs in heterozygous regions. An alternate assembly always accompanies a primary assembly. It is not useful by itself as it is fragmented and incomplete.
