LT1, an ONT Long-read-based Assembly Scaffolded with Hi-C Data and Polished with Short Reads

Overview

Journal GigaByte

Date 2023 Feb 24

PMID 36824523

Authors

Hui-Su Kim

Asta Blazyte

Sungwon Jeon

Changhan Yoon

Yeonkyung Kim

Changjae Kim

Dan Bolser

Ji-Hye Ahn

Jeremy S Edwards

Jong Bhak

Affiliations

Soon will be listed here.

Abstract

We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female 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.

Citing Articles

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

Kim H, Blazyte A, Jeon S, Yoon C, Kim Y, Kim C GigaByte. 2023; 2022:gigabyte51.

PMID: 36824523 PMC: 9650228. DOI: 10.46471/gigabyte.51.

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