HoCoRT:主体污染去除工具
Ignas Rumbavicius1, Trine B Rounge2,3, Torbjørn Rognes4,5
1Centre for Bioinformatics, Department of Informatics, University of Oslo, PO Box 1080 Blindern, 0316, Oslo, Norway.
BMC bioinformatics
|October 2, 2023
概括
HoCoRT是一种新的工具,可以有效地从中枪元基因组数据中去除宿主污染. 它提供了速度和准确性,优于现有的微生物组分析方法.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 步枪元基因组测序容易受到宿主生物的污染.
- 移除宿主序列对于准确的微生物组分析至关重要,减少偏差和计算负载.
- 现有的主机删除工具往往过时或难以使用.
研究的目的:
- 开发HoCoRT,这是一个快速和用户友好的工具,可以从元基因组数据中优化移除宿主序列.
- 评估HoCoRT中实施的各种宿主清除方法的速度和准确性.
- 根据阅读长度和微生物群类型,为最佳宿主清除策略提供建议.
主要方法:
- HoCoRT是一个开源的命令行工具,用于移除主机污染.
- 它使用各种映射,分类和对齐方法 (例如BioBloom,Bowtie2,HISAT2,Kraken2,Minimap2).
- 使用合成和公共的人体肠道和口腔微生物群数据集进行了评估,这些数据集具有短和长的读数.
主要成果:
- HoCoRT提供了一个用户友好的界面,提供基因组索引和方法选择的选项.
- 对于简短的阅读,BioBloom,Bowtie2和HISAT2为肠道微生物提供了最佳的速度/准确性;Kraken2是最快但更不准确的.
- 对于长时间的读数,Kraken2和Minimap2获得了最高的准确性 (59%的人类读数被检测到).
结论:
- 对于移除主机,HoCoRT比DeconSeq更快,更准确一些.
- 推的最佳方法因读数长度和微生物群类型而异.
- 作为一个Bioconda包,HoCoRT提供开源代码和麻省理工学院许可证.
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