Resubmission

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, Rein Leetmaa, Juvid Aryaman, Aurora Gómez-Durán, 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)
bayesian inference of mitochondrial parameters
integration of mtDNA information with gene-expression data with scanpy
identification of differentially expressed genes
raw sequencing data is not provided by references are given. Pre-computed data is provided to reproduce results.