MiTo

MiTo is a user-friendly Python package enabling interactive, single-cell, lineage-informed, multi-omic analysis.

MiTo’s capabilities include:

1. Preprocessing of scLT data (particular focus on MAESTER <10.1038/s41587-022-01210-8> technology)

2. Phylogeny and clonal inference

3. Downstream analysis and visualization

Implemented in accordance with the scverse guidelines and integrating with other popular single-cell packages (e.g., anndata, scanpy, cassiopeia), MiTo adds the “lineage” modality encoded in naturally occurring mitochondrial DNA (mtDNA) variants (MT-SNVs) to python single-cell workflows.

MiTo core functionalities have been implemented into nf-MiTo, a Nextflow pipeline for scalable MT-SNVs-based single-cell lineage tracing.