Reproducibility scripts for mumemto

February 13, 2025 · View on GitHub

Mumemto is a tool for analyzing pangenome sequence collections. It identifies maximal unique/exact matches (multi-MUMs and multi-MEMs) present across a collection of sequences. Mumemto can visualize pangenome synteny, identify misassemblies, and provide a unifiying structure to a pangenome.

Preprint available at https://doi.org/10.1101/2025.01.05.631388.

This repo contains scripts to recreate the results reported in the preprint. The main software repo is available at https://github.com/vikshiv/mumemto. These scripts are intended for use with Mumemto v1.1.0.

How to use this repo

Each figure has a collection of scripts to reproduce the corresponding figure in the paper. The assembly data for each experiment can be found here. For each bash script, change the path at the top to match the data path.

See references below for the original assembly sources. HPRC assemblies were scaffolded with RagTag.

Figure 2

First run the two bash scripts in graph_construction to build the Minigraph-Cactus comparison graph and the Mumemto-based graphs. Then to generate Fig 2H, use the jupyter notebook in fig2.

Figure 3

First generate the multi-MUM information using mumemto with the bash script in fig3. Then use the two jupyter notebooks to recreate Fig3.

Figure 4

First generate the multi-MUM information using mumemto with the bash script in fig4. Then use the included jupyter notebooks to recreate Fig4.

References

  • W.-W. Liao, M. Asri, J. Ebler, D. Doerr, M. Haukness, G. Hickey, S. Lu, J. K. Lucas, J. Monlong, H. J. Abel, et al., “A draft human pangenome reference,” Nature, vol. 617, no. 7960, pp. 312–324, 2023.
  • D. Tang, Y. Jia, J. Zhang, H. Li, L. Cheng, P. Wang, Z. Bao, Z. Liu, S. Feng, X. Zhu, et al., “Genome evolution and diversity of wild and cultivated potatoes,” Nature, vol. 606, no. 7914, pp. 535–541, 2022.
  • Potato Database, http://solomics.agis.org.cn/potato/, Accessed: 2024-12-10.
  • G. Hickey, J. Monlong, J. Ebler, A. M. Novak, J. M. Eizenga, Y. Gao, T. Marschall, H. Li, and B. Paten, “Pangenome graph construction from genome alignments with Minigraph-Cactus,” Nature Biotechnology, pp. 1–11, 2023.