Question: Does Cell Ranger DNA support non-human genomes?
Answer: Cell Ranger DNA development has been focused entirely on human cells and data. Creation of libraries from non-human species and subsequent analysis is not supported, and should be considered experimental.
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. We offer pre-built human and mouse references, although we do not offer any mouse datasets.
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.