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Automated assembly of centromeres from ultra-long error-prone reads


Centromeric variation has been linked to cancer and infertility, but centromere sequences contain multiple tandem repeats and can only be assembled manually from long error-prone reads. Here we describe the centroFlye algorithm for centromere assembly using long error-prone reads, and apply it to assemble human centromeres on chromosomes 6 and X. Our analyses reveal putative breakpoints in the manual reconstruction of the human X centromere, demonstrate that human X chromosome is partitioned into repeat subfamilies and provide initial insights into centromere evolution. We anticipate that centroFlye could be applied to automatically close remaining multimegabase gaps in the reference human genome.

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Fig. 1: centroFlyeHOR pipeline.
Fig. 2: centroFlyemono pipeline.
Fig. 3: Information about cenX assemblies.
Fig. 4: Comparison of read mappings between the centroFlye, centroFlyedel, T2T4 and T2T6 assemblies.
Fig. 5: Coverage plots for centroFlye, centroFlyedel, T2T4 and T2T6 assemblies.
Fig. 6: Coverage of various cenX assemblies by discordant reads.

Data availability

centroFlye centromere 6 and X assemblies and all supporting data is available at Zenodo: The ONT reads that were generated by the T2T consortium are deposited under accession number PRJNA559484.

Code availability

The codebase of the algorithm is available at The version of centroFlye that generates the assemblies described in the paper is in the branch: cF_NatBiotech_paper_Xv0.8.3-6v0.1.3. Jupyter notebooks for reproducing all figures in this study are provided in the Github repository


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We are indebted to I. Alexandrov, M. Kolmogorov, K. Miga and V. Shepelev for many insightful comments that improved centroFlye algorithm. We are grateful to A. Bankevich, A. Bzikadze, T. Dvorkina, A. Mikheenko, A. Phillippy, C. Wu and J. Yuan for helpful discussions and suggestions.

Author information




Both authors contributed to developing centroFlye algorithm and writing the paper. A.V.B. implemented centroFlye algorithm. P.A.P. directed the work.

Corresponding author

Correspondence to Pavel A. Pevzner.

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The authors declare no competing interests.

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Supplementary Information

Supplementary Notes 1–7 and Figs. 1–5.

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Bzikadze, A.V., Pevzner, P.A. Automated assembly of centromeres from ultra-long error-prone reads. Nat Biotechnol 38, 1309–1316 (2020).

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