Question: Does Cell Ranger DNA support non-human genomes?
Answer: At this time, only these human and mouse references have seen extensive testing for Cell Ranger DNA. We offer pre-built human and mouse references, although we do not offer any mouse datasets.
Although we have not conducted performance benchmarking on non-human samples, we do enable analysis of non-human data in the software by providing cellranger-dna mkref, a utility to build a Cell Ranger DNA compatible reference from a user-supplied reference file in FASTA format.
The product is likely to work better on genomes that are similar in size to the human genome. Microbial genomes are orders of magnitude smaller than human so the product may not work well for microbial genomes.
Since Cell Ranger DNA will only report on mappable regions of the genome, highly repetitive genomes will have proportionally less of the genome interrogated by the analysis, i.e. less of the genome will be effectively visible.