Read classification using database of single pangenome

[snayfach]

I'm interested in performing ultra-fast classification of metagenomic reads against a database that contains a single pangenome (thousands of genomes of the same species). My goal is to identify the subset of reads in a metagenome in FASTQ format that might come from my genome of interest. I care a lot more about sensitivity than specificity. Would kaiju be a good choice for this problem?