K-mer Analysis estimate genome size for selected s


分析模块,采用基于K-mer统计的分析方法来估计基因组大小。封装了Software: KmerGenie。

KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie's choices lead to assemblies that are close to the best possible over all k-mer lengths.

分析模块引用了 kmergenie-1.7016 软件(http://kmergenie.bx.psu.edu/)。


Chikhi R., Medvedev P. Informed and Automated k-Mer Size Selection for Genome Assembly, HiTSeq 2013. [on arXiv]