Submission

The first release of the analysis pipeline as discussed in the manuscript
"Cryptic mitochondrial ageing takes a lifetime and is pathophysiologically informative in single cells across tissues and species" by Alistair Green*, Florian Klimm* Aidan S. Marshall, Juvid Aryaman, Patrick F. Chinnery, and Nick S. Jones.

Contains all functionality to reproduce results:

• alignment of raw reads with STAR
• identification of mtDNA mutations
• characterization of these mtDNA mutations to identify cryptics
• further statistical analysis of these (e.g., site-frequency spectrum, selection effects, accumulation with age)
• integration of mtDNA information with gene-expression data with scanpy
• Iddentification of differentially expressed genes

Raw sequencing data is not provided by references are given. Pre-computed data is provided to reproduce results.