I have a question about the use of alignment-free tools like Kallisto or Salmon for bacterial RNA-seq transcript quantification. Bacterial genomes are gene-dense and have a significant proportion of overlapping genes, but no splicing/introns.
What advantages / disadvantages (in terms of accuracy / biases) would alignment-free tools have for bacterial transcriptomes compared to more traditional alignment-based tools like Bowtie + featureCounts? Do they have problems with overlapping (convergent or divergent) genes?
Computation speed is not a major consideration because the bacterial genomes are small and don't have splicing.
Any insights would be appreciated.
I added Salmon as tag to attract its developer @Rob.