The two most common approaches to sequencing genomes, are clone-based (hierarchical) and whole genome shotgun (WGS) sequencing. In the clone-based method, genomic DNA is cut into large random segments (150-200kb). Each segment is inserted into a Bacterial Artificial Chromosome (BAC). The BAC is sequenced using a shotgun sequencing approach where the BAC DNA is sheared into smaller random pieces (2-4kb). From each piece two reads will be generated, one from each end, these are referred to as read pairs. The reads (~4000/BAC) along with their orientation and distance information are used to assemble the BAC. The completed sequence of a genome is obtained by using a BAC clone map to order and orient the BAC clone sequences into a contiguous piece, chromosome or genome.

In the whole-genome shotgun sequencing method, genomic DNA is sheared and sequenced as with BAC sequencing, but millions of reads are generated and used in the assembly of the genome. Mapping data and comparison to related genomes helps in assembling the genome correctly. Both methods of assembly can be complicated by sequencing errors, clone biases, repetitive genome structures, and polymorphisms.

At WUGSC, based on the genome complexity and sequencing objective, we select a proper sequencing strategy from the hierarchical, WGS or a combination of the two methods. For assembly of BAC-sized clones, we use the Phrap assembler developed by Phil Green. WGS assemblies of large genomes are generated with PCAP developed in collaboration with Xiaoqiu.