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用于对从PacBio HiFi和ONT reads获得的植物基因组进行支架搭建的Hi-C工具的基准测试。

Benchmarking of Hi-C tools for scaffolding plant genomes obtained from PacBio HiFi and ONT reads.

作者信息

Obinu Lia, Trivedi Urmi, Porceddu Andrea

机构信息

Department of Agricultural Sciences, University of Sassari, Sassari, Sardinia, Italy.

Edinburgh Genomics, The University of Edinburgh, Edinburgh, United Kingdom.

出版信息

Front Bioinform. 2024 Nov 15;4:1462923. doi: 10.3389/fbinf.2024.1462923. eCollection 2024.

DOI:10.3389/fbinf.2024.1462923
PMID:39619774
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11604747/
Abstract

The implementation of Hi-C reads in the genome assembly process allows the ordering of large regions of the genome in scaffolds and the generation of chromosome-level assemblies. Several bioinformatics tools have been developed for genome scaffolding with Hi-C, and each tool has advantages and disadvantages that need to be carefully evaluated before their adoption. We generated two assemblies of obtained from the same raw PacBio HiFi and Oxford Nanopore Technologies data. We scaffolded the assemblies implementing Hi-C reads with the scaffolders 3D-DNA, SALSA2, and YaHS, with the aim of identifying the tool providing the most accurate assembly. The scaffolded assemblies were evaluated according to contiguity, completeness, accuracy, and structural correctness. In our analysis, YaHS proved to be the best-performing bioinformatics tool for scaffolding genome assemblies in .

摘要

在基因组组装过程中使用Hi-C读取数据，能够对基因组中的大片段区域进行支架排序，并生成染色体水平的组装结果。已经开发了几种用于利用Hi-C进行基因组支架构建的生物信息学工具，每个工具都有其优缺点，在采用之前需要仔细评估。我们从相同的原始PacBio HiFi和牛津纳米孔技术数据生成了两个组装结果。我们使用支架构建工具3D-DNA、SALSA2和YaHS，通过实施Hi-C读取数据来构建组装结果的支架，目的是确定提供最准确组装的工具。根据连续性、完整性、准确性和结构正确性对构建好支架的组装结果进行评估。在我们的分析中，YaHS被证明是在[具体物种或基因组]中构建基因组组装支架的性能最佳的生物信息学工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/69ec/11604747/6fc46e452e4e/fbinf-04-1462923-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/69ec/11604747/8352d04349e0/fbinf-04-1462923-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/69ec/11604747/a25aeeb4a4ae/fbinf-04-1462923-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/69ec/11604747/6fc46e452e4e/fbinf-04-1462923-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/69ec/11604747/8352d04349e0/fbinf-04-1462923-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/69ec/11604747/a25aeeb4a4ae/fbinf-04-1462923-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/69ec/11604747/6fc46e452e4e/fbinf-04-1462923-g003.jpg

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Bioinformatics. 2023 Jan 1;39(1). doi: 10.1093/bioinformatics/btac808.
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Efficient iterative Hi-C scaffolder based on N-best neighbors.基于 N-最佳邻居的高效迭代 Hi-C 支架。
BMC Bioinformatics. 2021 Nov 27;22(1):569. doi: 10.1186/s12859-021-04453-5.
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Tiara: deep learning-based classification system for eukaryotic sequences.Tiara：基于深度学习的真核序列分类系统。
Bioinformatics. 2022 Jan 3;38(2):344-350. doi: 10.1093/bioinformatics/btab672.
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High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads.利用纳米孔和高保真长读长进行高质量拟南芥基因组组装
Genomics Proteomics Bioinformatics. 2022 Feb;20(1):4-13. doi: 10.1016/j.gpb.2021.08.003. Epub 2021 Sep 3.
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