Next-Gen sequencing

Magazine


Ribodepletion - where is the catch?

Clients of our sequencing laboratory often require the preparation of sequencing libraries using rRNA depletion (ribodepletion), ie including rRNA removal. As we sometimes find that the results of rRNA removal are unsatisfactory, we performed tests described below.



Combining Illumina and ONT reads makes your de novo assembly successful

Although state-of-the-art Next-Generation sequencing (NGS) technologies generate an adequate amount of sufficient quality data for de novo genome assembly of organisms for which the reference sequence is not known yet, the genome assembly process itself is still a major challenge for bioinformaticians. In this article, we will try to outline the issue of assembly and show possible solutions.



Our sequencing experience on MiSeq at 2x300 b

Illumina sequencing technology is commonly referred to as short-read technology. In practice this means that it typically produces reads of hundreds of bases in length. Its current technological maximum in terms of read length is a kit for the MiSeq system that allows reading up to 600 b (2x300 setting). In this article, we have taken a closer look at some of the problems associated with this type of sequencing.



Quantity and quality of GridION data

In the last article we have described some features and consequent limitations of Sequel sequencer (Pacific Biosciences). If you are looking for an alternative to this long read technology, you might be considering the technology of Oxford Nanopore.



Quantity and quality of Sequel data

Pacific Biosciences SMRT sequencing technology enables sequencing of fragments of both tens of kilobase and hundreds of bases in length.



Sequencing low-diversity libraries on Illumina

Illumina sequencing technology is currently dominating the market. It offers a number of advantages over other technologies but unfortunately this does not mean that it is completely free of imperfections.



New horizons for Next-Generation Sequencing with GemCode technology (10x Genomics)

Our constant search for the best and most appropriate solutions to various experimental designs has led us to the introduction of the GemCode technology into our portfolio of Next-Generation sequencing services. In this post, we are happy to announce its availability to our clients and provide its basic description.



Several good reasons why Qubit is better than Nanodrop when quantifying your samples for NGS library prep

If I had a nickel for every time we answered the “How should I quantify my DNA or RNA for NGS library prep?” question, I wouldn’t need to be writing this article. I’d be on a boat in the Mediterranean. But since I’m not on a boat anywhere, I thought I could perhaps collect several good reasons why using Nanodrop is not really the best way of doing this.



A few thoughts on data analysis

The technology of next-generation sequencing produces huge amounts of data compared to Sanger technology. Its volume naturally depends on the design of the experiment, but primarily on the output capacity of the instrument. In principle, it is always necessary to deal with the transfer of large amounts of data into a form which enables their effective processing to allow a deeper analysis of the sequences obtained which is the very aim of the experiment.


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