Quick and easy 2nd order genome assembly: Syntenic Path Assembly using CoGe

With ever decreasing costs of DNA sequencing comes the opportunity for anyone to sequence the genome of any organism they wish.  However, the transformation of these raw data into usable information requires computational tools; ideally, computational systems that make these transformations available for any scientist.  The comparative genomics platform, CoGe, provides access to over 20 web-based tools for analyzing and comparing genomes.  One of CoGe’s tools, SynMap, provides the means to generate whole genome comparisons to identify syntenic genomic regions.  SynMap’s primary data visualization system relies on syntenic dotplots to identify and characterize syntenic regions.  One of option SynMap’s options, the Syntenic Path Assembly, uses syntenic information to orient and order contigs from a de novo genome assembly to an assembled reference genome, creating a pseudoassembly of a genome which can be exported as chromosomal pseudomolecules.  This hybrid genome assembly approach surmounts some of the limitations of exclusive reference genome and de novo assembly methods. 

Of particular interest, this approach works well not only for closely related genomes, but also for distally related genomes.   This workshop will demonstrate the use of the Syntenic Path Assembly option in SynMap on closely related bacterial genomes, and on distally related plant genomes (diverged ~90MYA). This latter case is an example whereby a plant genome is sequenced and assembled into a very low-quality draft assembly using less than $3000 of data and iPlant’s resources.

CoGe: http://genomevolution.org
Syntenic Path Assembly: http://genomevolution.org/wiki/index.php/Syntenic_path_assembly