KoNA: Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data

Abstract

During the last decade, the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges, including access to human data, as well as transfer, storage, and sharing of enormous amounts of data. To promote data-driven biological research, the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station (K-BDS), which consists of multiple databases for individual data types. Here, we introduce the Korean Nucleotide Archive (KoNA), a repository of nucleotide sequence data. As of July 2022, the Korean Read Archive in KoNA has collected over 477 TB of raw next-generation sequencing data from national genome projects. To ensure data quality and prepare for international alignment, a standard operating procedure was adopted, which is similar to that of the International Nucleotide Sequence Database Collaboration. The standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline, followed by manual examination. To ensure fast and stable data transfer, a high-speed transmission system called GBox is used in KoNA. Furthermore, the data uploaded to or downloaded from KoNA through GBox can be readily processed using a cloud computing service called Bio-Express. This seamless coupling of KoNA, GBox, and Bio-Express enhances the data experience, including submission, access, and analysis of raw nucleotide sequences. KoNA not only satisfies the unmet needs for a national sequence repository in Korea but also provides datasets to researchers globally and contributes to advances in genomics. The KoNA is available at https://www.kobic.re.kr/kona/.

1. Introduction

The drastic price decrease of next-generation sequencing (NGS) data and improvement of sequencing platforms with higher data throughput have resulted in the production of more than tens of petabases of raw sequencing data [1,2]. For example, in Korea, a few petabases of NGS data in diverse biological systems have been generated from several national projects, such as the Korea Post-Genome Project. To deposit, store, and share the enormous amount of raw nucleotide sequence data, there have been many efforts to construct repository databases by national and international data centers, such as the National Center for Biotechnology Information (NCBI), the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI), the DNA Data Bank of Japan (DDBJ), and the National Genomics Data Center (NGDC) [3–6]. These publicly available repositories provide datasets to global scientific communities and facilitate data reuse, which can reduce costs and usher advances in genomics.

Despite the impressive contribution of these repositories, additional national repositories are emerging in many countries mainly for three reasons. First, many countries are carrying out nationwide genome projects and producing huge amounts of data that need to be archived. Second, domestic networks have larger upload and download bandwidths, enabling faster data transfer than international networks. Third, deposition of and access to human data are controlled by domestic laws because of the sensitive nature of human data [4,6]. The Korea BioData Station (K-BDS), which was developed by the Korea Bioinformation Center (KOBIC), is a data archive that was initiated to address these three reasons.