Assemble Anaeroplasma species genome from whole genome sequencing

[Amro]

Hi everyone,

I have a fasta file containing reads generated by PacBio whole genome sequencing of a feces sample from mouse. I need to extract the reads which belong to the Anaeroplasma species and generate an assembled circularized Anaeroplamsa genome. I am familiar with Linux and R. I would very much appreciate your advice on the needed steps and the required tools or R packages.

Many thanks