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kmergenie website  

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.

Environment Modules

Run module spider kmergenie to find out what environment modules are available for this application.

System Variables



If you publish research that uses kmergenie you have to cite it as follows:

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