Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh.
Department of Computer Science and Engineering, United International University, Dhaka, Bangladesh.
PLoS One. 2021 Jan 7;16(1):e0245058. doi: 10.1371/journal.pone.0245058. eCollection 2021.
Genome wide association studies (GWAS) attempt to map genotypes to phenotypes in organisms. This is typically performed by genotyping individuals using microarray or by aligning whole genome sequencing reads to a reference genome. Both approaches require knowledge of a reference genome which hinders their application to organisms with no or incomplete reference genomes. This caveat can be removed by using alignment-free association mapping methods based on k-mers from sequencing reads. Here we present an improved implementation of an alignment free association mapping method. The new implementation is faster and includes additional features to make it more flexible than the original implementation. We have tested our implementation on an E. Coli ampicillin resistance dataset and observe improvement in execution time over the original implementation while maintaining accuracy in results. We also demonstrate that the method can be applied to find sex specific sequences.
全基因组关联研究（GWAS）试图在生物体内将基因型映射到表型。这通常通过使用微阵列对个体进行基因分型，或者通过将全基因组测序reads 与参考基因组对齐来完成。这两种方法都需要参考基因组的知识，这限制了它们在没有或不完全参考基因组的生物中的应用。通过使用基于测序reads 的 k-mer 的无比对关联映射方法，可以消除此限制。本文介绍了一种改进的无比对关联映射方法的实现。新的实现更快，并且包含更多的功能，使其比原始实现更灵活。我们已经在大肠杆菌氨苄青霉素抗性数据集上测试了我们的实现，并观察到执行时间相对于原始实现的提高，同时保持了结果的准确性。我们还证明该方法可用于查找性别特异性序列。
