本篇文章主要讲了组装和对比中的组装,从头测序和重测序中的从头测序。介绍了从头组装的算法。 文中的所有的课件均来自南京医科大学 邵娇芳老师,笔记为个人整理 靶向DNA序列捕获技术新趋势 A rapid CRISPR/Cas9-mediated, amplification-free target enrichment method for native-strand sequencing* image.png image.png...
K-mer 用途 用于基因组从头组装前的基因组调查,评估基因组的大小。 基因组大小可以由(总 K-mer 数量)/(K-mer 期望测序深度)来估计,通常以 ==K-mer 分布曲线的 主峰深度==作为期望测序深度 K-merr频数统计分布图解读 在测序覆盖均匀、不存在测序误差和基因组重复序列的理论条件下,K-mer分布曲...
In one method, the k-mers are separated into one or more groups followed by removing k-mers common to the groups. In another method, k-mers are removed based on a selected taxonomic threshold level. A third method combines the features of the previous two methods. The methods are ...
Then, the Gapped k-mer calculation method which is based on quad-tree is also introduced. Conclusions >From the prediction results, this method not only reduces the dimension, but also improves the prediction precision of protein subcellular localization....
We provide our method, termed Poregen, as a generalisable approach for creation of custom, de novo k-mer models for nanopore signal data analysis. AVAILABILITY AND IMPLEMENTATION. Poregen is an open source package under an MIT licence: https://github.com/hiruna72/poregen SUPPLEMENTARY ...
membranaceus had obvious hybridity peak by K-mer method, and the hybridity percentage as high as 2.1%. Conclusion The genome size of A. membranaceus was about 1.45 Gb and the heterozygosity is high. These data would provide a reference for the genomic research in A. membranaceus. [中图分类...
decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metag...
The method is called distance-based conservative k-mer searching algorithm (DCKS) which is based on the conservation of k-mer pair distance. 通过对TRANSFAC数据库中转录因子结合位点(TFBS)所包含核苷k联体(k-mer)在人类和小鼠基因组启动子区中分布的比较分析,提出一种在人类全基因组启动子区搜索转录调节...
Finally we show that besides the smaller size of a minimum SPSS, it also has advantages in downstream applications. As an example of ak-mer-based method, we query our compressed representation with the tools SSHash [45] and Bifrost [23]. These are state-of-the-art tools supportingk-mer-...
We compared the microbiota composition associated to temperature changes using ASV dataset (r=0.52, p=0.022), KTU dataset (r=0.75, p<0.001), and the original results of paper (OTU clustering method; r=0.72, p< 0.001).The 16S amplicon denoising method unbiased picks high-quality sequence ...