Can I use bwa to align metagenome pacbio reads to several reference genome? Or are there any other tools to achieve metagenome alignment for pacbio reads?
You don't use bwa to run against multiple genomes at once, but you could of course manually align your sequencing data to multiple genomes 1 by 1 using bwa mem or minimap2. Furthermore, for actual metagenome alignment tools, I would look at this paper:
http://ccb.jhu.edu/people/salzberg/docs/Breitwieser-etal-2017-Metagenomics-review-reprint.pdf
As your question is more complicated than a simple yes or no. To do what you are asking properly there are several things to take into account (which are all discussed in this review).
You will want to look at the readQC metrics as well as the metagenome alignment section (and maybe even metagenome assembly).
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If you already know the genome(s) that could be present in your sample then you can use minimap2 to align reads to the genome(s).
Another approach would be to carry out denovo assembly using canu and then search the contigs against reference databases using either BLAST or DIAMOND.