Spoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this major human pathogen. Spoligotypes can be predicted from short read genome sequencing data; however, no methods exist for long read sequence data such as from Nanopore or PacBio. We present a novel software package Galru, which can rapidly detect the spoligotype of a Mycobacterium tuberculosis sample from as little as a single uncorrected long read. It allows for near real-time spoligotyping from long read data as it is being sequenced, giving rapid sample typing. We compare it to the existing state of the art software and find it performs identically to the results obtained from short read sequencing data. Galru is freely available from https://github.com/quadram-institute-bioscience/galru under the GPLv3 open source licence.

中文翻译：

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使用Galru从未经校正的长时间阅读中快速进行结核分枝杆菌基因分型

结核分枝杆菌的Spoligotyping提供了这种主要人类病原体的亚种分类。可以从短读的基因组测序数据中预测Spoligotypes。但是，不存在用于读取长序列数据的方法，例如Nanopore或PacBio。我们提出了一个新颖的软件包Galru，它可以快速检测结核分枝杆菌样本的spoligotype，而只需进行一次未校正的长时间阅读即可。它允许对长读取的数据进行测序时进行近乎实时的分型，从而快速进行样品分型。我们将其与现有技术水平进行比较，发现其性能与从短读测序数据中获得的结果相同。根据GPLv3开源许可，可以从https://github.com/quadram-institute-bioscience/galru免费获得Galru。