LT1, an ONT long-read-based assembly scaffolded with Hi-C data and polished with short reads

Hui-Su Kim; Asta Blazyte; Sungwon Jeon; Changhan Yoon; Yeonkyung Kim; Changjae Kim; Dan Bolser; Ji-Hye Ahn; Jeremy S Edwards; Jong Bhak

doi:10.46471/gigabyte.51

LT1, an ONT long-read-based assembly scaffolded with Hi-C data and polished with short reads

GigaByte. 2022 May 4:2022:gigabyte51. doi: 10.46471/gigabyte.51. eCollection 2022.

Authors

Hui-Su Kim¹, Asta Blazyte^{1

2}, Sungwon Jeon^{1

2

3}, Changhan Yoon^{1

2}, Yeonkyung Kim^{1

3}, Changjae Kim³, Dan Bolser⁴, Ji-Hye Ahn³, Jeremy S Edwards⁵, Jong Bhak^{1

2

3

4}

Affiliations

¹ Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
² Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
³ Clinomics LTD, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
⁴ Geromics Ltd., Suite 1, Frohock House, 222 Mill Road, Cambridge, CB1 3NF, UK.
⁵ Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA.

Abstract

We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly, constructed using 57× nanopore long reads and polished using 47× short paired-end reads. We utilized 72 GB of Hi-C chromosomal mapping data for scaffolding, to maximize assembly contiguity and accuracy. The contig assembly of LT1 was 2.73 Gbp in length, comprising 4490 contigs with an NG50 value of 12.0 Mbp. After scaffolding with Hi-C data and manual curation, the final assembly has an NG50 value of 137 Mbp and 4699 scaffolds. Assessment of gene prediction quality using Benchmarking Universal Single-Copy Orthologs (BUSCO) identified 89.3% of the single-copy orthologous genes included in the benchmark. Detailed characterization of LT1 suggests it has 73,744 predicted transcripts, 4.2 million autosomal SNPs, 974,616 short indels, and 12,079 large structural variants. These data may be used as a benchmark for further in-depth genomic analyses of Baltic populations.

Grants and funding

This work was supported by the U-K BRAND Research Fund (grant number 1.200108.01) of Ulsan National Institute of Science & Technology (UNIST), and the research project was funded by the UNIST Ulsan City Research Fund (grant number 1.200047.01). This work was also supported by the Promotion of Innovative Businesses for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea; grant numbers: P001193 (1425157301) (2.220036.01). This work was also supported by the Establishment of Demonstration Infrastructure for Regulation-Free Special Zones fund (MSS, Korea) (P0016191) (2.220037.01) and (1425157253) by the Ministry of SMEs and Startups. JB and CK were partially supported by Clinomics Inc. and the Genome Research Foundation.