Efficient strategies for de novo sequencing of small, mid-size and large eukaryotic genomes
Obtain high quality genome de novo assemblies by sequencing a combination of shotgun libraries and long paired-end libraries.
Eurofins MWG Operon offers libraries with wide jumping distances to easily tackle any genome size - from bacterial genomes to large and complex eukaryotic genomes.
- Long paired-end (LPE) libraries to be sequenced on GS FLX / GS FLX+
- Long jumping distance (LJD) libraries to be sequenced on Illumina HiSeq 2000
- LPE and LJD libraries are available with jumping distances of 3 kbp, 8 kbp, 20 kbp and 40 kbp
The LPE or LJD fragments comprise of 2 DNA fragments originally 3 kbp, 8 kbp, 20 kbp or 40 kbp apart in the genome of interest. The long paired-end reads are used to determine the orientation and relative position of the contigs generated during the data assembly of shotgun reads. With Eurofins MWG Operon’s unique library portfolio, spanning gaps or repeats in your genome of up to 40 kbp is achieved in a fast and efficient manner.
Working closely together with our customers, we perform de novo genome sequencing projects in the following stages:
- Ultra high throughput sequencing of a shotgun library and assembly into contigs
- Scaffolding of contigs by long paired-end sequencing
- Optional, closing of gaps based on Sanger technology
- Optional, bioinformatic analysis, e.g. annotation or comparison of different organisms
The appropriate layout of different LJD or LPE libraries as well as the sequencing technology depends mainly on the genome size. We would be happy to advise you about the most convenient strategy.
Are you interested in an individual quote or need additional information? Just contact us!
LPE libraries up to 40kb - enhance your assemblies
The long paired-end (LPE) library, designed for the Roche 454 technology, span gaps and repeats up to 40 kbp to further enhance the assembled data.
Eurofins MWG Operon's long paired-end (LPE) libraries offer excellent scaffolding solutions. Our LPE libraries comprise DNA fragments with an adaptor sequence. The 2 adaptor flanking sequences are segments of DNA originally located approximately 3 kbp, 8 kbp, 20 kbp or 40 kbp apart from each other on the genome of interest (see sidebar figure).
Span gaps or repeats in the genome of up to 40 kbp in a fast and, efficient manner. The paired-end reads are mapped to contigs derived from shotgun sequencing. When both reads map to distinctive contig ends, these are bridged. As a result, the LPE libraries provide both high quality sequence information of the genome as well as scaffolding information of most contigs.
If you have further questions about our libraries or need specific information for your project, just contact us!
Long jumping distance libraries
Achieve high throughput scaffolding using our proprietary long jumping distance (LJD) libraries.
Based on our long-term expertise with long paired-end (LPE) libraries, we developed LJD libraries adapted to the Illumina HiSeq 2000 technology.
Mate-pair libraries have no recognition site to mark the crossover between 2 fragment ends. LJD libraries harbour several advantages over the mate-pair libraries since they contain a spacer to tag the crossover point (see figure in sidebar). Find a list of the advantages below.
Span large repeats in your genome
We offer LJD libraries with 3 kbp, 8 kbp, 20 kbp and even 40 kbp jumping distances to resolve large and complex repetitive structures.
The Illumina mate-pair library is available with a jumping distance of only 2 kbp to 5 kbp.
No misassembly with chimeric reads
Our LJD libraries have a built in spacer to prevent misassemblies due to chimeric reads when changeover occurs during sequencing. The spacer defines the exact location where a changeover occurs thus offering a physical separation between both fragment ends.
The mate-pair protocol does not offer a physical separation between the two fragment ends. Therefore, sequencing of a mate-pair library will generate a huge quantity of hybrid reads that contain sequence information from one and the other end of the original fragment. These reads can lead to severe misassemblies.
LJD reads with proven insert size
The spacer of the LJD library prevents incorrect classifications. Depending on the spacer location, the two reads can immediately be marked as LJD reads with proven insert size.
Shotgun like paired-end reads can occur when not all unbiotinylated fragments are washed away in the library preparation procedure (see figure in sidebar). These read pairs have a gap size of only 300-500 bp. They do not contribute to bridge large repeats and the wrong classification can lead to misassemblies.
If you have further questions about our libraries or need specific information for your project, just contact us!
NGS Favourites - straightforward solutions for complex projects
Next generation sequencing service packages predesigned for your application
The Favourites represent optimised solutions, that evolved from the vast array of custom projects in the last 5 years.
- The Favourites are developed for sequencing on either GS FLX+ or HiSeq 2000
- The Favourites contain all steps from library preparation to bioinformatic analysis
Advantages:
- Highest quality - the NGS Favourites are based on superior in-house techniques which ensure premium data quality
- Economic prices - expertise combined with attractive prices
- Straigthforward solution - save time and effort by choosing a Best Practise approach that includes all steps to successfully finalise your project
Test one of our NGS Favourites for genome sequencing and explore the easy way of Next Generation Sequencing with Eurofins MGW Operon as your professional project partner:
Shotgun sequencing with Sanger-like read length
- Shotgun library preparation from chromosomal DNA
- Sequencing with either 1/4, or 1/2, or 2x1/2 Roche GS FLX+ technology
- De novo data assembly and data delivery of FASTA/sff files
Economy Genome Sequencing Favourite
- Designed for genomes up to 3 Mbp, 5 Mbp or 8.5 Mbp
- Shotgun and long paired-end (LPE) 3 kbp library preparation
- Sequencing on Roche GS FLX+ and GS FLX
- Data assembly and delivery
Premium Genome Sequencing Favourite
- Designed for genomes up to 3 Mbp, 5 Mbp, 8.5 Mbp, 20 Mbp or 40 Mbp
- Shotgun and LPE 8 kbp library preparation
- Sequencing on Roche GS FLX+ and GS FLX
- Data assembly and delivery