* All trademarks are property of their respective owners.
Beckman Coulter and the stylized logo are registered trademarks of Beckman Coulter, Inc.
Whole Genome Sequencing
Beckman Coulter Genomics has generated whole genome sequences for a variety of organisms with a wide range of associated genome sizes. Factors considered for the best experimental design for a whole genome sequencing project include the size of the target genome, the anticipated complexity of the genome, the desired level of finishing, or completeness, and whether the genome requires de novo assembly or can be mapped against a published reference sequence.
Genome Resequencing
While any sequencing technology can be applied to a genome re-sequencing project the ultra-high throughput of the Roche* 454 GS FLX* and Illumina* HiSeq* 2000 next generation sequencing platforms makes them particularly powerful tools for resequencing large genomes with a reference sequence available for mapping.
Microbial Resequencing
For many bacterial species of interest, a type strain as well as other widely available laboratory strains have been sequenced. These reference strains are attractive genetic engineering subjects since derived strains can easily be compared at the genome level against the parental strain by using next generation sequencing. Because of its high throughput and long read lengths, the Roche 454 technology provides the best price/performance ratio for bacterial genome sequencing. For viral genomes, reads will be generated on either the Roche 454 or Illumina platforms, depending on the application.
De novo Genome Sequencing
De novo sequencing is used to sequence uncharacterized genomes where there is no reference sequence available, or known genomes where significant structural variation is expected. De novo sequence reads are typically generated on the Roche 454 (taking advantage of the long read lengths) or Illumina HiSeq 2000 platforms. Sequence reads from multiple platforms can also be combined (e.g., Illumina + 454) for cost effective coverage of large genomes, or with Sanger sequencing reads for genomes with particularly abundant or complex repeats.
Microbial de novo Sequencing
Certain species of interest call for a de novo sequencing approach because no parental strains are available or because acquisition of genetic material or rearrangements may have important consequences on the properties of the experimental strains. If the species has a relatively conserved overall genome organization, a cost effective fragment library approach may be used, while for genomes known for high plasticity using a 3 kb mate-pair library instead is recommended. High GC organisms call for a combined fragment/mate-pair sequencing approach.
For publication ready microbial genome sequencing Beckman Coulter Genomics uses a pipeline that supports hybrid assemblies allowing for the use of Roche 454 and Illumina sequencing to ensure coverage over the whole genome at high quality.
Results
Genome mapping or assembly is overseen by Beckman Coulter Genomics bioinformatics professionals. Results are delivered via a secure FTP site or are shipped on a portable hard drive depending upon the size of the dataset. Analyses of next generation sequencing data are typically performed with proprietary tools provided by the vendor of the respective technology. Resulting file types, data formats and associated read quality metrics may be platform specific.
Getting Started
Beckman Coulter Genomics project managers will work with you to ensure appropriate study design for your project. This design will accommodate your specific needs and include recommendations for sample preparation and data analysis options. Please contact Beckman Coulter Genomics to discuss your next project.
