Cas9-Enabled single cell lineage tracing tree reconstruction

Cassiopeia is a software suite for processing CRISPR/Cas9-based lineage tracing sequencing data into phylogenies. The software contains three modules for (a) preprocessing sequencing reads into “character matrices”; (b) reconstructing phylogenies from these character matrices; and (c) providing analysis tools for deriving insights from these phylogenies. The core methodology is described in our publication entitled “Inference of Single-Cell Phylogenies from Lineage Tracing Data”.

You can view and install the tool from GitHub.

Relevant publications

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts.
JJ. Quinn*, MG. Jones*, RA. Okimoto, S. Nanjo, MM. Chan, N. Yosef†, TG. Bivona†, JS. Weissman†
Science , 2021
bioRxiv preprint
Inference of Single-Cell Phylogenies from Lineage Tracing Data.
MG. Jones*, A. Khodaverdian*, JJ. Quinn*, MM. Chan, JA. Hussmann, R. Wang, C. Xu, JS. Weissman†, N. Yosef†
Genome Biology , 2020
Molecular recording of mammalian embryogenesis.
MM. Chan, ZD. Smith, S. Grosswendt, H. Kretzmer, TM. Norman, B. Adamson, M. Jost, JJ. Quinn, D. Yang, MG. Jones, A. Khodaverdian, N. Yosef, A. Meissner, JS. Weissman
Nature , 2019