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TALLYMER | A method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

A flexible and memory-efficient collection of programs for k-mer counting and indexing of large sequence sets. Unlike previous methods, Tallymer is based on enhanced suffix arrays. This gives a much larger flexibility concerning the choice of the k-mer size. Tallymer can process large data sizes of several billion bases. We used it in a variety of applications to study the genomes of maize and other plant species.

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TALLYMER classification

TALLYMER specifications

Unique identifier:
OMICS_02096
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Perl
Stability:
Stable

TALLYMER distribution

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Credits

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Publications

Institution(s)

Center for Bioinformatics, University of Hamburg, Hamburg, Germany; Cold Spring Harbor Lab, Cold Spring Harbor, NY, USA; Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA

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