STRONG: metagenomics strain resolution on assembly graphs.
STRONG: metagenomics strain resolution on assembly graphs.
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DOI：
10.1186/s13059-021-02419-7
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发表时间：
2021-07-26
期刊：
影响因子：
12.3
通讯作者：
Darling AE
中科院分区：
文献类型：
--
作者：
Quince C;Nurk S;Raguideau S;James R;Soyer OS;Summers JK;Limasset A;Eren AM;Chikhi R;Darling AE
我们介绍了装配图上的序列分辨率（STRONG），它从多个宏基因组样本中重新识别菌株。STRONG执行共组装，并分仓成宏基因组组装的基因组（MAG），并在变体简化之前存储共组装图。这使得能够提取每个MAG中的单个单拷贝核心基因（SCG）的子图及其单位样本覆盖率。贝叶斯算法BayesPaths确定存在的菌株数量、它们在SCG上的单倍型或序列以及丰度。STRONG使用合成群落进行验证，并且对于真实的厌氧生物反应器时间序列，生成与从长Nanopore读取中观察到的那些相匹配的单倍型。在线版本包含补充材料，可在（10.1186/s13059-021-02419-7）获得。
We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads. The online version contains supplementary material available at (10.1186/s13059-021-02419-7).