Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy
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Galaxy 中可扩展、可访问且可重复的参考基因组组装和评估
DOI：
10.1038/s41587-023-02100-3
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发表时间：
2024
影响因子：
46.9
通讯作者：
Rabbani, Keon
中科院分区：
文献类型：
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作者：
Larivière, Delphine;Abueg, Linelle;Brajuka, Nadolina;Gallardo-Alba, Cristóbal;Grüning, Bjorn;Ko, Byung June;Ostrovsky, Alex;Palmada-Flores, Marc;Pickett, Brandon D.;Rabbani, Keon
地球生物基因组计划的目标是在未来十年内为所有~ 180万已知的真核生物物种产生参考基因组。实现这一目标将需要参考基因组生产的当前速度增加至少两个数量级1。为了实现这一加速，将需要装配过程的自动化，以及任何研究小组都可以广泛访问的管道。实现这一目标需要在三个主要领域持续努力：基因组组装优化和最佳实践开发、计算基础设施供应以及传播和培训。为了优化组装过程并设计最佳实践，我们结合了两个项目的专业知识-脊椎动物基因组计划（VGP）和欧洲参考基因组图谱（ERGA）。VGP是一项合作努力，旨在为所有~ 70，000种脊椎动物物种生成参考基因组5。在过去的5年中，VGP已经发布了数百个新的参考基因组，这些基因组得到了自动化组装工具和工作流程的支持。ERGA是一项泛欧洲科学倡议，旨在为所有约200，000种欧洲真核生物物种生成参考基因组，其中许多物种都在国际自然保护联盟濒临灭绝物种红色名录2上。从之前的VGP工作中取得进展，最初在DNanexus平台上（补充说明，第1.1节），我们在银河系生态系统6中开发了一个管道，将太平洋生物科学公司（PacBio）的高保真（HiFi）读取与Hi-C地图和/或光学地图，以产生几乎完整的组件（补充说明1.3）。该管道进一步使用来自亲本的Hi-C或全基因组序列数据来分别产生染色体水平或全基因组水平的定相基因组。为了简化装配过程并确保质量，管道包括广泛的质量控制（QC）功能
The Earth BioGenome Project aims to produce reference genomes for all~ 1.8 million known eukaryotic species over the next decade 1–4. Achieving this goal will require the current pace of reference genome production to increase by at least two orders of magnitude 1. Automation of the assembly process with a pipeline that is widely accessible to any research group will be required to achieve this speed-up. Enabling this goal requires sustained effort in three major areas: genome assembly optimization and best-practice development, computational infrastructure provisioning, and dissemination and training. To optimize the assembly process and devise best practices, we combined the expertise of two projects—the Vertebrate Genomes Project (VGP) and the European Reference Genome Atlas (ERGA). The VGP is a collaborative effort to generate reference genomes for all~ 70,000 vertebrate species 5. In the past 5 years, the VGP has released hundreds of new reference genomes supported by the development of automated assembly tools and workflows 1, 5. The ERGA is a pan-European scientific initiative to generate reference genomes for all~ 200,000 European eukaryote species, many of which are on the International Union for Conservation of Nature Red List of species at risk of extinction 2.Advancing from the prior VGP work, originally on the DNAnexus platform (Supplementary Note, section 1.1), we developed a pipeline within the Galaxy ecosystem 6 that combines Pacific Biosciences (PacBio) high-fidelity (HiFi) reads with long-distance information from Hi-C maps and/or optical maps to generate nearly complete assemblies (Supplementary Note 1.3). The pipeline further uses Hi-C or whole-genome sequence data from parents to produce chromosomal-level or whole-genome-level phased genomes, respectively. To streamline the assembly process and ensure quality, the pipeline includes extensive quality control (QC) functions