In a new study, researchers have developed a way to dramatically improve the ability to sequence the DNA of an organism that can’t be cultured in the laboratory, such as bacteria living in the human gastrointestinal tract or living in the depths of the ocean. This is the next generation sequencing technology. It will have a profound impact on the operation of the metagenomics sequencing.
This method called TruSPADES assembled short reads with 300 base pairs produced by machine into synthetic long reads. The synthetic long reads are made of about 10,000 base pairs in the genome.
The researchers say that the use of these synthetic long sequence segments rather than the short sequence segments to assemble the genome is like using the entire chapter rather than a single sentence to assemble a book. Therefore, people have strong motivation to use long DNA sequencing to improve sequencing.
At present, as a leader in the market of long fragments, Pacific Biosciences or Oxford Nanopore does not generate accurate long sequencing fragments, and they are very difficult to solve complex problems such as assembly metagenome. Metagenome can refer to all the microbial genomes from natural environment samples, or also refer to all microbes from natural environment. In contrast, the accuracy of synthetic long sequence segments has increased by 100 times, and can be produced in large scale to cover most of the bacteria in the metagenome.
In order to develop new methods, researchers had obtained a short sequence of 300 to 100 base pairs with a bar code. They then used a common method in short read sequencing called de Brujin graph to describe these short fragments, so as to assemble into synthetic long sequence segments. This map allows researchers to determine which short fragments are connected together, so as to assemble a longer and more accurate synthetic long sequence segments.
It is especially challenging because researchers need to study hundreds of bacteria rather than one of them that live in a microbial community.
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