I am totally new to metatranscriptomics and apologised in advance if this has already been covered. I was wondering if anyone can recommend any packages/software suitable for mapping to multiple bacterial genomes simultaneously suitable for metatranscriptomics analysis (note: my average fastq size is ~30-35GB!)?
We previously ran our data in kraken and got an idea of what the most abundant bacteria are in the sample, but the specificity is only to the species level and not to individual strains. I then mapped the reads to the reference strain for each of the species that we are interested in one by one using bwa (default parameters), but we are worried that the reads we are getting might be due to cross-reactivity with other strains or other closely related species and aligning to multiple genomes simultaneously might reduce this issue.
Any suggestion will be greatly appreciated! Many thanks!