Applications
Eukaryote Whole Genome
Overview
The GS FLX System's ultra-high throughput, long reads enable comprehensive assembly of whole eukaryote genomes, including de novo assembly and assembly against a reference sequence. Combine shotgun long single reads (400 base pairs) and Long-tag Paired end reads (>100 base pairs each) from each end of a 3,000 bp span to effectively tackle complex eukaryotic genomes. The unbiased nature of the system results in more comprehensive sequence information than traditional Sanger sequencing. Coming Soon: GS FLX Titanium series paired end reads with 3K-20K spans.
Publications:
- Wheeler et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872-876. April 17, 2008.
Click here to see all Eukaryote Whole Genome publications.
Data Analysis Tools:
GS De Novo Assembler Software, GS Mapper Software
How it Works:
Shotgun Sequencing
For shotgun sequencing large-size genomic DNA samples are randomly fragmented into small 300- to 800-base-pair fragments via physical shearing. Addition of adapters to the generated fragments creates a library of DNA fragments which is immobilized on DNA capture beads and individually sequenced on a PicoTiterPlate device as shown in the workflow description (link to workflow). The generated sequences are then assembled into a number of unordered and unoriented contigs using the GS De Novo Assembler Software and a consensus sequence is generated.
Figure 1: Assembly of sequences into contigs using the GS De Novo Assembler Software
Paired-End Sequencing
After assembly of de novo shotgun sequencing reads into contigs the generated contigs are ordered and oriented using paired-end reads. These paired-end reads have two 100-mer DNA segments on each side (paired ends) that were originally located either 3 kb, 8 kb, or 20 kb apart in the sequence of interest. The GS De Novo Assembler Software enables subsequent mapping of the 100-mer fragments to the generated contigs and thus ordering and orienting of the contigs into scaffolds. This combined information provides a high-quality draft sequence of the genome.
Figure 2: Ordering and orienting of contigs via paired-end reads