BinChecker: a new algorithm for quality assessment of microbial draft genomes
BinChecker: a new algorithm for quality assessment of microbial draft genomes
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BinChecker：一种用于微生物基因组草图质量评估的新算法
DOI：
10.1101/2021.10.01.462745
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发表时间：
2021
期刊：
影响因子：
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通讯作者：
Peter Meinicke
中科院分区：
文献类型：
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作者：
Heiner Klingenberg;Peter Meinicke
在从元基因组序列数据重建微生物基因组时，对最终的完整性和可能的污染的估计是质量控制的关键。在元基因组学中，候选基因组通常从元基因组组装和随后组装的重叠群的结合中获得。BinChecker提供了一种新的质量评估方法，该方法基于快速的蛋白质结构域搜索和用于识别标记结构域(特征)集的聚类方法。用于估计的特征集不是针对给定的参考基因组数据库预先计算的，而是通过自适应聚类和特征选择为每个bin单独找到的。特别是，自适应方便了底层数据库的创建和扩展，只需要添加参考基因组的蛋白质特征图谱。模拟垃圾箱的测试表明，BinChecker的预测精度符合当前的技术水平，同时在速度和灵活性方面提供了显著的优势。
In the reconstruction of microbial genomes from metagenomic sequence data, the estimation of the final completeness and possible contamination is crucial for quality control. In metagenomics candidate genomes are usually obtained from a metagenome assembly and a subsequent binning of the assembled contigs. BinChecker provides a novel approach to quality assessment that is based on a fast protein domain search and a clustering approach for identification of marker domain (“feature”) sets. The feature sets that are used for estimation are not pre-computed for a given database of reference genomes, but are individually found for each bin by adaptive clustering and feature selection. In particular, the adaptivity facilitates the creation and extension of the underlying database, which just requires to add protein feature profiles of reference genomes. Tests with simulated bins indicate that the prediction accuracy of BinChecker meets the current state of the art while providing significant advantages in terms of speed and flexibility.
DOI：
10.1093/bioinformatics/btu843
发表时间：
2015-05-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
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作者：
Meinicke P
通讯作者：
Meinicke P