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De Novo Sequencing Of Genomes

You want to sequence a new genome? We recommend long reads

Achieve best quality genome de novo assemblies using a PacBio long read technology platform.

Long reads are essential for assembling genomes. Only long continuous stretches can span all sorts of repetitive regions in your genome and result in high quality assemblies with a reasonable number of contigs.

Working closely together with our customers, we perform de novo genome sequencing projects in the following stages:

  • Preparation of SMRTbell libraries with maximal insert size using BluePippin size selection
  • Sequence SMRTbell libraries on PacBio RSII
  • Large genomes: Eventually supplement with Illumina shotgun reads
  • Optional, bioinformatic analysis, e.g. assembly (only small genomes), annotation or comparison of different organisms

Are you interested in an individual quote or need additional information? 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 libraries, we developed LJD libraries adapted to the Illumina HiSeq 2500 technology.

LJD libraries (see figure) harbour several advantages over the Illumina mate-pair libraries since they contain a spacer to tag the crossover point between both fragments. Find a list of the advantages when sequencing using with LJD libraries 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 hybrid reads

Our LJD libraries have a built in spacer to prevent misassemblies when changeover occurs within the (hybrid) read. The spacer defines the exact location where a changeover occurs thus offering a physical separation between both fragment ends.

The Illumina mate-pair protocol and other mate-pair protocols built on it do 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

Adjustments in the LJD pull-down protocol highly reduces the number of shotgun paired-end reads. With LJD libraries only about 1% of reads are shotgun read pairs.

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. Contamination rate of Illumina mate-pair reads with shotgun read pairs is usually about 2-5%, sometimes up to 30%.

If you have further questions about our libraries or need specific information for your project, just contact us!