MHConstructor：针对 MHC 组装难题的高通量、单体型信息解决方案

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-10-17 DOI:10.1186/s13059-024-03412-6

Kristen J. Wade, Rayo Suseno, Kerry Kizer, Jacqueline Williams, Juliano Boquett, Stacy Caillier, Nicholas R. Pollock, Adam Renschen, Adam Santaniello, Jorge R. Oksenberg, Paul J. Norman, Danillo G. Augusto, Jill A. Hollenbach

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引用次数: 0

摘要

人类主要组织相容性复合体（MHC）的遗传多态性极高，这限制了基于参考的比对方法在序列组装中的实用性。我们将一种短线程、从头组装算法纳入工作流程，将其新颖地应用于 MHC。MHConstructor 是一个容器化的管道，设计用于高通量、单体型信息、可重复的全基因组测序组装和大型人群队列中目标捕获短读数数据的组装。迄今为止，还没有其他独立的工具能从短线程数据中生成全新的 MHC 组合。MHConstructor 有助于广泛获取高质量、免比对的 MHC 序列分析。

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MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge

The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short-read, de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target capture short-read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short-read data. MHConstructor facilitates wide-spread access to high-quality, alignment-free MHC sequence analysis.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.