Department of Electrical & Computer Engineering, University of California, San Diego, La Jolla, 92093, CA, USA.
Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
Genome Biol. 2019 Feb 13;20(1):34. doi: 10.1186/s13059-019-1632-4.
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.
在快速的气候和生物多样性变化时代，能够廉价地描述分类多样性至关重要。最近的基因组掠过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数据绝大多数的核 DNA。相比之下，我们建议使用所有未组装的读取。我们引入了一种无组装和无比对的工具 Skmer，用于计算查询和参考基因组掠过之间的基因组距离。Skmer 在估计距离和识别参考数据集的最近匹配方面表现出出色的准确性。
