Tag Archives: long jumping distance libraries

How to benefit from our superior LJD’s on the MiSeq

With the update of our MiSeq system to 250 bp reads genome sequencing on this system gets even more important. But long reads and huge data output are not the only prerequisite for a great de novo assembly result.

What is missing?

Paired-end libraries that span gaps and repetitive structures can improve de novo genome assemblies tremendously. Our proprietary long jumping distance libraries (LJDs) are perfectly suited for scaffolding on Illumina sequencing devices. In contrast to other paired-end libraries (like Illumina mate pair library), our LJD library preparation involves an adaptor-guided ligation of the genomic fragments. The different preparation protocol offers the following advantages:

  • No hybrid reads – a unique sequence identifies the crossover points
  • No shotgun pairs – less than 1% of all LJD reads are shotgun paired-end reads
  • Distinct insert sizes – we prepare LJDs with 3, 8, 20 or even 40 kbp insert size
  • Span large repeats – large and complex repeats up to 40 kbp can be resolved

Mapped reads: All reads from a 3 kbp LJD library (grey) are aligned to a reference sequence. Two LJD read pairs are highlighted (blue + black) and their measured insert size is 3107 bp and 3002 bp respectively.


Why should I combine MiSeq long reads and LJDs?

The new features of the MiSeq (250 bp reads; data output up to 8 Gbp) enable the combined and cost-efficient approach of shotgun and LJD libraries in one run. The MiSeq output is sufficient to sequence several bacterial genomes or single fungal genomes (up to 60 Mbp) with appropriate coverage.

  • Longer reads – more sequence information to correctly map the reads onto your contigs
  • Short delivery time – due to the shorter run time compared to the HiSeq 2000

Read more about our long jumping distance libraries on our website

Which sequencing strategy do you use for scaffolding of contigs?

In our latest poll that started mid of November 2011 we raised the question about your sequencing strategies for scaffolding projects. 29 ngs-expert.com readers did submit their votes.

39% of all votes agree my own opinion that LPE and LJD libraries are the preferred method for scaffolding of contigs. Long reads of up to 40 kbp can be easily and efficiently bridged.

But despite that, it is also obvious that all other techniques are still used for scaffolding projects. And I am still interested to see whether this might change with the new C2 chemistry for PacBio RS that is announced for Q1.

Why Choose LJD Libraries Rather Than Mate-Pair Libraries?

Why should you choose long jumping- distance (LJD) libraries rather than mate-pair libraries, especially for de novo sequencing projects? There is a simple answer to this question: Because the resulting data are much more suitable for de novo assembly and scaffolding.

Why is this so? Mate-pair libraries contain higher percentage of undesired inward-facing read-pairs (if you are not familiar with inward and outward facing reads, just take a look into our FAQs on this subject). These reads are not mate-pair (in other words they are shotgun paired-end). The portion of such reads in the LJD library is greatly reduced.

Furthermore, if using mate pair libraries, it is not clear, if (and if yes, where) there is the changeover within the resulting reads. In other words: A read may contain sequence from one AND the other end without knowing where the changeover is. As a result chimeric reads go into the assembly. This effect is almost completely eliminated if LJD libraries are used, because of the differences in library generation.

Which experiences did you gain with LJD or mate-pair libraries? I’d be happy to hear from you.