KmerGenie

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Description

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

  • HPC_KMERGENIE_DIR




Citation

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