There is a need to determine which genome assembler is the best one for assembling bacterial organisms:
- New bacterial strains have been sequenced on a daily basis due to development of Human Microbiome Project, among others.
- Goal of assembling bacterial organisms is different from the goal of assembling giant organisms. While assembling giant genomes aims at getting a draft global assembly, assembling bacterial organisms aims at accurate local assemblies to enable comparison of different species/strains in order to find differences between pathogenic and non-pathogenic strains.
- Some genome assemblers perform better on large genomes while other assemblers work better on small organisms; however, all assemblers are being used to assemble bacterial organisms.
GAGE-B also aims at answering the following questions:
- Which parameters should be used to generate the optimal assemblies?
- How does coverage level impact assembly?
- Can high covereage by a single library replace multi-library assemblies?
- Are better assemblies generate by HiSeq or MiSeq Illumina reads?
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