arXiv 2602.167282026-02-17q-bio.GN

FUNGAR：一种从宏基因组短读数据直接检测抗真菌耐药突变的管道

FUNGAR: a pipeline for detecting antifungal resistance mutations directly from metagenomic short reads

ResGen – One Health Antimicrobial Resistance Genomic Surveillance Initiative（ResGen - 一健康抗菌素耐药基因组监测倡议）；Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil（巴西南里奥格兰德联邦大学生物分子与生物技术系生物科学研究所）；Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil（巴西南里奥格兰德联邦大学生物技术中心细胞与分子生物学研究生项目）

Henrique RM Antoniolli, Lívia Kmetzsch, Charley C Staats

阅读 PDF

arXiv 页面 ↗HTML 原文 ↗

AI总结：

FUNGAR是一种开源管道，用于从宏基因组短读数据中快速检测抗真菌耐药基因和突变，通过DIAMOND比对和FungAMR数据库实现高效识别。

摘要：

动机：抗真菌耐药性已成为临床和环境健康领域日益严峻的全球性问题。从测序读取中直接检测已知的耐药突变，特别是在宏基因组样本中，仍是一个主要挑战。由于真菌病原体往往比细菌病原体被忽视，大多数可用工具都是为细菌设计的，而针对真菌的工具通常需要组装的基因组。在宏基因组数据集中，基于组装的策略可能会因基因组碎片化、低丰度物种或对耐药位点的不完全恢复而造成大量信息丢失。结果：本文介绍了FUNGAR，一种开源管道，用于从短读数据快速识别抗真菌耐药基因和突变。FUNGAR使用DIAMOND进行翻译比对，并利用FungAMR数据库中的精修数据，以检测所有六个开放阅读框中的氨基酸替换。该管道生成结构化、可重复的报告，将检测到的变异与相关抗真菌药物联系起来，并可以轻松定制用于新物种或数据库。

英文摘要：

Motivation: Antifungal resistance has become an increasing global concern in both clinical and environmental health. Detecting known resistance mutations directly from sequencing reads, in special metagenomic samples, remains a major challenge. As fungal pathogens are often neglected compared with bacterial pathogens, most available tools are designed for bacterial taxa, whereas tools targeting fungi typically require assembled genomes. In metagenomic datasets, assembly-based strategies may result in substantial information loss due to genome fragmentation, low-abundance species, or incomplete recovery of resistance loci. Results: Here, we present FUNGAR, an open-source pipeline for the rapid identification of antifungal resistance genes and mutations directly from short-read data. FUNGAR employs translated alignments with DIAMOND and curated data from the FungAMR database to detect amino acid substitutions across all six open reading frames. The pipeline produces structured, reproducible reports linking detected variants to their associated antifungal drugs and can be easily customized for new species or databases.

机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。