RIBAP：细菌核心基因组综合注释管道，用于物种水平以上的泛基因组计算。

IF 12.3 1区生物学 Q1 Agricultural and Biological Sciences

Genome Biology Pub Date : 2024-07-01 DOI:10.1186/s13059-024-03312-9

Kevin Lamkiewicz, Lisa-Marie Barf, Konrad Sachse, Martin Hölzer

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引用次数: 0

摘要

微生物泛基因组分析可确定原核生物基因组中存在或不存在的基因。然而，目前的工具在分析序列多样性较高的物种或较高的分类次序（如属或科）时受到限制。Roary ILP 细菌核心注释管道（RIBAP）使用整数线性规划方法来完善 Roary 预测的基因簇，以确定核心基因。RIBAP 成功地处理了衣原体、克雷伯氏菌、布鲁氏菌和肠球菌基因组的复杂性和多样性，在属一级鉴定包罗万象的核心基因方面优于其他已有的和最新的泛基因组工具。RIBAP 是免费提供的 Nextflow 管道，可在 github.com/hoelzer-lab/ribap 和 zenodo.org/doi/10.5281/zenodo.10890871 上下载。

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RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level.

Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such as genera or families. The Roary ILP Bacterial core Annotation Pipeline (RIBAP) uses an integer linear programming approach to refine gene clusters predicted by Roary for identifying core genes. RIBAP successfully handles the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, outperforming other established and recent pangenome tools for identifying all-encompassing core genes at the genus level. RIBAP is a freely available Nextflow pipeline at github.com/hoelzer-lab/ribap and zenodo.org/doi/10.5281/zenodo.10890871.

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来源期刊

Genome Biology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-GENETICS & HEREDITY

CiteScore

25.50

自引率

3.30%

发文量

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.