Phân tích bộ gen
Analysis of Short-read Aligners using Genome Sequence Complexity
2020 Dec 16 KSE 2020
Quang Tran, Nam Sy Vo, Eric Hicks, Tin Nguyen, Vinhthuy Phan
Next generation sequencing technologies have the capability to provide large numbers of short reads inexpensively and accurately. Researchers have proposed many different methods to align short reads to reference genomes. Nevertheless, long repeats, which are known to be abundant in eukaiyotic genomes, have caused considerable difficulty for genome assembly methods that rely on short-read alignment. Although a few researchers have studied sequence complexity of genomes in terms of repeats, none have quantitatively related such complexity to the difficulty of short read alignment and assembly. In this paper, we investigate several measures of genome sequence complexity with the goal of quantifying...
Read more articleA comprehensive and bias-free evaluation of genomic variant clinical interpretation tools
2021 Dec 28 KSE 2021
Nguyen Minh Trang, Mai Nguyen Anh Vu, Tran Hoang Anh, Do Minh Nguyet, Nguyen Thanh Nguyen
The advancement of Next Generation Sequencing (NGS) generates a huge pool of raw sequencing data and genomic variants, while the diverse selection of variant annotation tools adds even more confusion to the mix. Choosing the right tools for clinical interpretation of genomic variants is still challenging due to the lack of comprehensive evaluation studies in this field. Here, we introduced a bias-free analysis approach to assess ten well-known variant annotation tools in terms of clinical interpretation. Our results revealed notable correlations of contemporary methods when applied to the Clin Var dataset. Moreover, allele frequency is still a strong predictor, emphasizing...
Read more articleA comprehensive imputation-based evaluation of tag SNP selection strategies
2021 Dec 28 KSE 2021
Dat Thanh Nguyen, Hieu Quang Dinh, Giang Minh Vu, Duong Thuy Nguyen, Nam Sy Vo
Regardless of the rapid development of sequencing technology, single nucleotide polymorphism (SNP) array has been widely used for many large-scale genomic studies due to its cost-effectiveness. Recently, in parallel with the advancement in imputation strategies, several genotyping platforms for various species have been developed. Despite the importance of imputation accuracy in SNP array design, to the best of our knowledge, there are no systematic studies for evaluating tag SNP selection methods based on this metric. In this paper, using the leave-one-out cross-validation approach on the 1000 genome high-coverage dataset, we comprehensively evaluated four well-known tag SNP selection algorithms based on...
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