Department of Electrical & Computer Engineering, University of Thessaly, 38221, Volos, Greece.
Hellenic Pasteur Institute, 11521, Athens, Greece.
Genome Biol. 2022 Jan 31;23(1):39. doi: 10.1186/s13059-022-02610-4.
We introduce AGAMEMNON ( https://github.com/ivlachos/agamemnon ) for the acquisition of microbial abundances from shotgun metagenomics and metatranscriptomic samples, single-microbe sequencing experiments, or sequenced host samples. AGAMEMNON delivers accurate abundances at genus, species, and strain resolution. It incorporates a time and space-efficient indexing scheme for fast pattern matching, enabling indexing and analysis of vast datasets with widely available computational resources. Host-specific modules provide exceptional accuracy for microbial abundance quantification from tissue RNA/DNA sequencing, enabling the expansion of experiments lacking metagenomic/metatranscriptomic analyses. AGAMEMNON provides an R-Shiny application, permitting performance of investigations and visualizations from a graphics interface.
我们引入了 AGAMEMNON（https://github.com/ivlachos/agamemnon），用于从鸟枪法宏基因组和宏转录组样本、单微生物测序实验或测序宿主样本中获取微生物丰度。AGAMEMNON 以属、种和菌株分辨率提供准确的丰度。它采用了一种时间和空间高效的索引方案，用于快速模式匹配，使具有广泛可用计算资源的大型数据集能够进行索引和分析。宿主特异性模块为从组织 RNA/DNA 测序中定量微生物丰度提供了出色的准确性，从而能够扩展缺乏宏基因组/宏转录组分析的实验。AGAMEMNON 提供了一个 R-Shiny 应用程序，允许通过图形界面进行调查和可视化。
