Production Assemblies
With the exception of the simplest genomes, the assembly process
involves a certain amount of human intervention. Modern assembly
programs are complex systems that need to be tuned to the specific
characteristics of the genome being assembled. Information
about the genome being assembled, such as genome size, repeat content,
or the presence of polymorphisms, is used to choose the correct
parameters for the assembly algorithm. Such information is
frequently not known and has to be gleaned from the results of
preliminary assemblies and specialized analyses of the shotgun
data. Often times, the data provided to the assembler has to be
cleaned up to satisfy the standards required by an assembly program.
The assembly of a complex genome is often performed in an iterative
fashion, as researchers continuously tune the assembly program to
obtain the best results.
The lab notes detail the special techniques used for that genome.
Assembly Projects
A selection of the assemblies our team has contributed to. See the Genome Assembly page for more information.
Fruit Fly Endosymbionts
Steven Salzberg and colleagues identified the sequence of the bacterial
endosymbiont Wolbachia pipientis
within the publicly available sequence data of several species of fruit
fly. These results were reported in the open access journal
Genome Biology:
Salzberg,
S.L., Hotopp, J.C., Delcher, A.L., Pop, M., Smith, D.R., Eisen, M.B.,
Nelson, W.C. (2005) Serendipitous discovery of Wolbachia
genomes in multiple Drosophila species. Genome Biol 6
(3):R23.
The assemblies of the endosymbiont genomes identified in this study can
be obtained below. The assemblies were performed with AMOScmp.
Wolbachia endosymbiont of Drosophila annanasae - GenBank
entry
Wolbachia endosymbiont of Drosophila simulans - GenBank
entry
Wolbachia endosymbiont of Drosophila willistoni - contigs
trace
IDs
*Assemblies completed in partnership with TIGR
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