Skmer: assembly-free and alignment-free sample identification using genome skims
Skmer: assembly-free and alignment-free sample identification using genome skims
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DOI：
10.1186/s13059-019-1632-4
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发表时间：
2019-02-13
期刊：
影响因子：
12.3
通讯作者：
Mirarab, Siavash
中科院分区：
文献类型：
--
作者：
Sarmashghi, Shahab;Bohmann, Kristine;Mirarab, Siavash
在这个气候和生物多样性迅速变化的时代，廉价描述分类多样性的能力至关重要。最近的基因组略读方法通过应用低通测序和计算恢复整个细胞器基因组，将当前的条形码实践扩展到短标记之外。这种方法丢弃了构成绝大多数数据的核DNA。相反，我们建议使用所有未组装的读段。我们介绍了一个组装免费和免费的工具，Skmer，计算查询和参考基因组略读之间的基因组距离。Skmer在估计距离和识别参考数据集中最接近的匹配方面表现出出色的准确性。
The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets.