A simple but effective method for strain-level characterisation of microbial samples using long read data is presented. The method, which relies on having a non-redundant database of reference genomes, differentiates between strains within species and determines their relative abundance. It provides markedly better strain differentiation than that reported for the latest long read tools. Good estimates of relative abundances of highly similar strains present at less than 1% are achievable with as little as 1Gb of reads. Host contamination can be removed without great loss of sample characterisation performance. The method is simple and highly flexible, allowing it to be used for various different purposes, and as an extension of other characterisation tools. A code body implementing the underlying method is freely available.

中文翻译：

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使用长时间阅读和MAPQ分数进行菌株级样品表征

提出了一种简单但有效的方法，该方法利用长时间读取的数据对微生物样品进行应变水平表征。该方法依赖于具有参考基因组的非冗余数据库，可区分物种内的菌株并确定其相对丰度。与最新的长读工具所报告的相比，它提供了明显更好的应变区分。只需低至1Gb的读取，就可以很好地估计高度相似菌株的相对丰度，其相对含量不到1％。可以去除宿主污染，而不会大大降低样品表征性能。该方法简单且高度灵活，允许将其用于各种不同目的，并作为其他表征工具的扩展。实现底层方法的代码体可免费获得。