engleski

Approaches to DNA de novo Assembly

DNA is the basic building block of all known life, accounting for all the diversities in nature. Determining the DNA of an individual organism is performed through a process called DNA sequencing. Although several different sequencing technologies do exist, they are limited and are able to acquire relatively short sequence reads. One of the approaches to sequencing involves randomly breaking a long DNA molecule into small fragments and sequencing only those fragments. Due to the random positioning of fragments on the source DNA, majority of them overlap, and provide the necessary information to combine them back together. The process of reconstructing the original DNA sequence from fragment reads is called DNA assembly. Assembly is a very computationally intensive process that may take days, or even weeks to produce the sequence of a more complex organism. Reconstructing a DNA sequence in the absence of a previously reconstructed reference sequence from a similar organism is called de novo assembly. De novo assembly methods currently provide the only means to discover new, previously unknown sequences, and are currently indispensable in biological research. In this paper, short descriptions of the sequencing process and the current sequencing platforms are given. DNA assembly process is thoroughly described, and the analysis of several de novo approaches used for assembly are presented. Overview and description of existing software tools are given, including some parallel implementations. As a conclusion, aspects of possible future development of DNA assembly are considered.

DNA sequencing; assembly; overlap; layout; consensus; de Bruijn; tools; parallel

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