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Detection of Copy Number Alterations Using Single Cell Sequencing
Published on: February 17, 2017
A high-precision genome size estimator based on the k-mer histogram correction
Xiangyu Liao1, Wufei Zhu2, Chaoyun Liu3
1Department of Oncology, Yichang Central People's Hospital, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China.
Introduction:
In the realm of next-generation sequencing datasets, various characteristics can be extracted through k-mer based analysis. Among these characteristics, genome size (GS) is one that can be estimated with relative ease, yet achieving satisfactory accuracy, especially in the context of heterozygosity, remains a challenge.
Methods:
In this study, we introduce a high-precision genome size estimator, GSET (Genome Size Estimation Tool), which is based on k-mer histogram correction.
Results:
We have evaluated GSET on both simulated and real datasets. The experimental results demonstrate that this tool can estimate genome size with greater precision, even surpassing the accuracy of state-of-the-art tools. Notably, GSET also performs satisfactorily on heterozygous datasets, where other tools struggle to produce useable results.
Discussion:
The processing model of GSET diverges from the popular data fitting models used by similar tools. Instead, it is derived from empirical data and incorporates a correction term to mitigate the impact of sequencing errors on genome size estimation. GSET is freely available for use and can be accessed at the following URL: https://github.com/Xingyu-Liao/GSET.
