I have metatranscriptomic data for several communities. When I use HISAT2 to align the reads from some of the pairings to a single genome I typically get near 50% of the reads aligning. There are a couple cases where near 100% of the reads align to a single genome. In these cases I am assuming that the genomes are very similar. Unfortunately I only have the whole genome sequence for one of the strains.
Is there a way to limit the amount of reads aligning to the wrong genome in HISAT2? My instinct is to increase the stringency of the alignment using the --score-min option. However I would like to hear from the community in case there is a more commonly used solution.