Protocol to identify fungal profile from fecal metagenomes in cancer patients prior to immunotherapy

被引：1

作者：

Huang, Xiaowen ^{[1
]}

Li, Lingxi ^{[1
]}

Chen, Haoyan ^{[1
]}

机构：

[1] Shanghai Jiao Tong Univ, Shanghai Inst Digest Dis, Shanghai Canc Inst, Sch Med,Div Gastroenterol & Hepatol,Renji Hosp,Sta, Shanghai, Peoples R China

来源：

STAR PROTOCOLS | 2024年 / 5卷 / 01期

基金：

中国国家自然科学基金;

关键词：

Bioinformatics; Cancer; Health Sciences; Microbiology;

D O I：

10.1016/j.xpro.2024.102847

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Identifying fungal profiles from metagenomes is challenging due to an incomplete fungal database and limitations in the understanding of software. Here, we describe a protocol for analyzing the fecal metagenome of cancer patients prior to immunotherapy. We describe steps for raw metagenomic sequencing data retrieval, human genome and contaminants elimination, and assigning taxonomy labels to fungal reads. We then detail measures for assessing fungal alpha diversity and beta diversity, along with differential analysis. For complete details on the use and execution of this protocol, please refer to Xiaowen Huang et al.1

引用

页数：13

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