Applications
Eukaryote Whole Genome
Overview
The Genome Sequencer FLX System enables comprehensive assembly of whole eukaryote genomes, including de novo assembly and assembly against a reference sequence. Combine 400 base shotgun reads and multi-span paired end reads (>150 base tags from each end of a 3 Kb, 8 Kb, or 20 Kb span) to effectively tackle complex eukaryotic genomes. Get the most complete genome coverage with long shotgun and 20 Kb span paired end reads, the longest of any next-generation system, ensuring contiguous sequence information over the highly repetitive regions of complex genomes. Reduce overall project time and cost by replacing the use of old, expensive and time consuming technologies such as fosmid and Sanger sequencing. Go further, faster than ever before in eukaryote genome sequencing.
Download flyer and view assembly data: De Novo Sequencing of Complex Genomes
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