How can I align a specific squence against fastq reads

Question

[Juliana]

Hi,

I would like to know which is the best tool to align a specific sequence against fastq reads from a WGS and afterwards determine the coverage depth.

The issue is that; I have my genome assembly from a bacterium and I only have one rRNA operon, it should be two rRNA operons. So, I would like to know the coverage of the region and/or to align my operon against fastq reads to determine if there is a mistake in the assembly.

Thanks