TY - JOUR

T1 - Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

AU - Mc Cartney, Ann M.

AU - Shafin, Kishwar

AU - Alonge, Michael

AU - Bzikadze, Andrey V.

AU - Formenti, Giulio

AU - Fungtammasan, Arkarachai

AU - Howe, Kerstin

AU - Jain, Chirag

AU - Koren, Sergey

AU - Logsdon, Glennis A.

AU - Miga, Karen H.

AU - Mikheenko, Alla

AU - Paten, Benedict

AU - Shumate, Alaina

AU - Soto, Daniela C.

AU - Sović, Ivan

AU - Wood, Jonathan M.D.

AU - Zook, Justin M.

AU - Phillippy, Adam M.

AU - Rhie, Arang

N1 - Mc Cartney, A.M., Shafin, K., Alonge, M. et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat Methods (2022). https://doi.org/10.1038/s41592-022-01440-3

PY - 2022/6

Y1 - 2022/6

N2 - Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first telomere-to-telomere human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Although derived from highly accurate sequences, evaluation revealed evidence of small errors and structural misassemblies in the initial draft assembly. To correct these errors, we designed a new repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly quality value from 70.2 to 73.9 measured from PacBio high-fidelity and Illumina k-mers. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both high-fidelity and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies.

AB - Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first telomere-to-telomere human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Although derived from highly accurate sequences, evaluation revealed evidence of small errors and structural misassemblies in the initial draft assembly. To correct these errors, we designed a new repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly quality value from 70.2 to 73.9 measured from PacBio high-fidelity and Illumina k-mers. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both high-fidelity and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies.

KW - Female

KW - Genome, Human

KW - High-Throughput Nucleotide Sequencing/methods

KW - Humans

KW - Nanopores

KW - Pregnancy

KW - Sequence Analysis, DNA/methods

KW - Telomere/genetics

UR - http://www.scopus.com/inward/record.url?scp=85127481319&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/bb4a1c9f-c9b3-3ff2-8982-8e1774c8edfe/

U2 - 10.1038/s41592-022-01440-3

DO - 10.1038/s41592-022-01440-3

M3 - Article

C2 - 35361931

AN - SCOPUS:85127481319

VL - 19

SP - 687

EP - 695

JO - Nature Methods

JF - Nature Methods

SN - 1548-7091

IS - 6

ER -