We assessed the performance of each GWAS approach based on loci for which the causal genes or variants were known from previous genetic studies. We found that k-mer-based GWAS was the most versatile approach and the best at pinpointing causal variants or candidate genes. Moreover, k-mer-...
k-mers方法的top特征关联强于SNP的top特征,甚至比在拟南芥或玉米中看到的更为强烈。 SNP- and k-mer-based GWAS in tomato. 结论:研究结果证明了k-mers结合GWAS的能力,可以检测出与表型变异相关的、更广泛的遗传变异。 本文提出了一种基于k-mers的GWAS方法,并将其与传统的基于SNP的方法直接比较了来自三个不同...
30], a previously developedk-mer-based motif discovery method, to ~ 3,000 human TF ChIP-seq samples across diverse TFs and cell types (Fig.1A). Each ChIP-seq sample was represented as a profile of TF-binding specificity scores (MOCCS2scores) for eachk-mer sequence, designated as a...
kGWASflow is a Snakemake workflow for performing k-mers-based GWAS. workflow bioinformatics gwas snakemake pipeline genomics ngs conda bioinformatics-pipeline structural-variation gwas-pipeline bioinformatics-tool gwas-tools kmers sciworkflows association-mapping Updated Jul 13, 2023 Python armin...
Kassemble is a Python package with the objective to assemble denovo contigs and scaffolds using a reference-free, k-mer based approach. kassemble incorporates the SPAdes software tool and/or SOAPdenovo2 tool as a Python wrapper to create contigs of unique k-mers extracted from reads in a fa...
Our algorithm first constructs the de Bruijn graph in linear time and then uses a Eulerian-cycle-based algorithm to compute the minimum representation, in time linear in the size of the output. Similar content being viewed by others Matchtigs: minimum plain text representation of k-mer sets ...
Further, several metagenome-wide association studies (M-GWAS) also underscored the effect of host genetics and host environment on the composition and functional potential of the gut microbiota [20], [21], [22]. This complex interplay of the microbial and host environments based on gene copy ...
SNP- and k-mer-based GWAS in tomato. 结论:研究结果证明了k-mers结合GWAS的能力,可以检测出与表型变异相关的、更广泛的遗传变异。 本文提出了一种基于k-mers的GWAS方法,并将其与传统的基于SNP的方法直接比较了来自三个不同基因组和种群特征的物种的2000多个表型——拟南芥、玉米和番茄。本研究颠覆了构建基因组...
Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to desig...
应用于细菌基因组的全基因组关联研究(GWAS)方法在发现遗传标记或详细评估标记效应方面显示了良好的结果。最近,基于k-mer组成的无比对方法证明了其探索副基因组的能力。然而,它们会导致冗余的描述和结果,有时很难解释。这里我们介绍DBGWAS,一个扩展的基于k-mer的GWAS方法,产生与不同表型相关的可解释的遗传变异。我们...