KmerGenie 1.7051 – K-mer size Selection for Genome Assembly

KmerGenie 1.7051

:: DESCRIPTION

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.

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::DEVELOPER

Rayan Chikhi, Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • R package
  • Python

:: DOWNLOAD

 KmerGenie

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jan 1;30(1):31-7. doi: 10.1093/bioinformatics/btt310. Epub 2013 Jun 3.
Informed and automated k-mer size selection for genome assembly.
Chikhi R1, Medvedev P.