Ensamblaje de genoma de Sphingobium yanoikuyae a partir de datos de secuenciación de Illumina y PACBIO archivados en la base de datos de NCBI

Abstract

Sphingobium yanoikuyae is a bacterium belonging to the Sphingomonadaceae family, it is characterized by the fact that it degrades several aromatic compounds, since it has enzymes that metabolize these contaminating compounds, therefore it has enormous potential to be used in bioremediation. Research was carried out to establish a pipeline for S. yanoikuyae genome assembly from Illumina and PACBIO sequences, stored at NCBI. Raw sequences were preprocessed by filtering and trimming; through the implementation of bioinformatics tools on the Galaxy and KBase platform; Quality control was done in FASTQC obtaining parameters such as the N50, the total assembly size and the number of contigs. Furthermore, assembly programs such as SPAdes, Megahit, Skesa or Velvet allowed an assembly to be carried out, however their results were not very precise or reliable; while, with Unicycler, a better assembly of the complete genome was obtained, highlighting the fused or hybrid assembly with 89 contigs and a length of 5402608 bp. Finally, Prokka was used for annotation, identifying 5045 genetic elements.