Ferramentas computacionais para a montagem de genomas bacterianos: um estudo comparativo

Abstract

The emergence of next generation sequencing technologies (NGS) has radically transformed the techniques for identifying the nitrogenous bases of DNA and has boosted the production of scientific research across the globe, especially in the field of sequencing and genetic analysis of bacteria. The post-sequencing step - the computational assembly of DNA fragments - is a complex process and highly dependent on the platforms on which the organisms were sequenced. This dependence, linked to several other factors, ended up creating favorable conditions for a large-scale production of assemblers of bacterial genomes, in which each one has different configurations and operating parameters. Furthermore, the choice of this tool is of paramount importance for the success of research in development. However, the scarcity of current works that deal with the performance of these software makes the choice of an assembler something difficult to be done. Given the above, this work proposes to develop a comparative study with 7 tools commonly used for the assembly of bacterial genomes, providing relevant information about the performance, implementation and usability of each one. All assemblers were tested with the same biological samples, obtained from the Sequence Read Archive (SRA) repository and from the second generation sequencing platform Ion Personal Genome Machine (IonPGM). In our study we tried to describe in detail how the assembly resources and strategies adopted by each program influenced its performance and the final quality of its results. For that, we use different metrics and quality parameters, resulting in more than 200 assemblies. In short, with this work we intend to provide bioinformatics professionals with sufficient information to guide them in choosing the appropriate tool for their projects, thus contributing to the advancement of techniques related to the assembly of bacterial genomes and in the development of scientific research in the area.