Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.

IF 12.3 1区 生物学 Q1 Agricultural and Biological Sciences Genome Biology Pub Date : 2022-09-08 DOI:10.1186/s13059-022-02743-6
Jamshed Khan, Marek Kokot, Sebastian Deorowicz, Rob Patro
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引用次数: 3

Abstract

The de Bruijn graph is a key data structure in modern computational genomics, and construction of its compacted variant resides upstream of many genomic analyses. As the quantity of genomic data grows rapidly, this often forms a computational bottleneck. We present Cuttlefish 2, significantly advancing the state-of-the-art for this problem. On a commodity server, it reduces the graph construction time for 661K bacterial genomes, of size 2.58Tbp, from 4.5 days to 17-23 h; and it constructs the graph for 1.52Tbp white spruce reads in approximately 10 h, while the closest competitor requires 54-58 h, using considerably more memory.

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使用Cuttlefish构建压缩de Bruijn图的可伸缩、超快速和低内存。
德布鲁因图是现代计算基因组学中的一个关键数据结构,其压缩变体的构建位于许多基因组分析的上游。随着基因组数据数量的快速增长,这往往会形成计算瓶颈。我们推出了“墨鱼2号”,大大提高了解决这一问题的技术水平。在商品服务器上,它将大小为2.58Tbp的661K个细菌基因组的图形构建时间从4.5天缩短到17-23小时;它在大约10小时内构建了1.52Tbp白云杉读数的图,而最接近的竞争对手需要54-58小时,使用了相当多的内存。
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来源期刊
Genome Biology
Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY
CiteScore
25.50
自引率
3.30%
发文量
0
审稿时长
14 weeks
期刊介绍: Genome Biology is a leading research journal that focuses on the study of biology and biomedicine from a genomic and post-genomic standpoint. The journal consistently publishes outstanding research across various areas within these fields. With an impressive impact factor of 12.3 (2022), Genome Biology has earned its place as the 3rd highest-ranked research journal in the Genetics and Heredity category, according to Thomson Reuters. Additionally, it is ranked 2nd among research journals in the Biotechnology and Applied Microbiology category. It is important to note that Genome Biology is the top-ranking open access journal in this category. In summary, Genome Biology sets a high standard for scientific publications in the field, showcasing cutting-edge research and earning recognition among its peers.
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