I have 100 metagenomic samples and a complete reference genome for Gardnerella vaginalis (14018).
I want a whole genome alignment of Gardnerella vaginalis for each metagenome, with the assumption that each alignment represents the population of Gardnerella vaginalis in each metagenome.
What tool would you recommend to create this fasta alignment by aligning metagenomic reads to a reference genome? And, how can I be confident that each read maps to the correct species (ie, only g. vaginalis reads map to g.vaginalis reference vs. lactobacillus reads mapping by accident)?
I have experience using bwa-mem2.