Genome annotation pipelines for prokaryotic and eukaryotic microorganisms using de novo short read genome assembly

Abstract

Next-generation sequencing (NGS) is the massively parallel sequencing technology that has revolutionized biological sciences. Currently, microorganism genomes have been widely studied using NGS. However, the lack of details in the draft or reference genome is a common problem in genome analysis. Therefore, this study aims to develop genome analysis pipelines for eukaryotic and prokaryotic microorganisms using public bioinformatics software and public databases. Leishmania matiniquensis and Leptospira interrogans were used as models for genome assembly and annotation in eukaryote and prokaryote, respectively. Our pipelines used SPAdes for short read assembled, AUGUSTUS and Prokka for gene prediction in eukaryotic and prokaryotic microorganisms, respectively. The various functional annotation databases and the eukaryotic and prokaryotic virulence factor gene databases were included in our pipelines. Finally, we hope these pipelines can be useful for the researcher who need to analyze and get the insight into gene information in the microorganism.