<![CDATA[BOL: Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive plant genomes]]> https://bioinformaticsonline.com/bookmarks/view/35619/tallymer-method-to-compute-k-mer-frequencies-and-its-application-to-annotate-large-repetitive-plant-genomes? https://bioinformaticsonline.com/bookmarks/view/35619/tallymer-method-to-compute-k-mer-frequencies-and-its-application-to-annotate-large-repetitive-plant-genomes Thu, 15 Feb 2018 10:21:02 -0600 https://bioinformaticsonline.com/bookmarks/view/35619/tallymer-method-to-compute-k-mer-frequencies-and-its-application-to-annotate-large-repetitive-plant-genomes <![CDATA[Tallymer: method to compute K-mer frequencies and its application to annotate large repetitive plant genomes]]> 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. In particular, Tallymer was used to index a set whole genome shotgun sequences from maize (B73) (total size 109 bp). 
Tallymer was effective in a variety of applications to aid genome annotation in maize, despite limitations imposed by the relatively low coverage of sequence available.

A manual can be found here.

Address of the bookmark: https://www.zbh.uni-hamburg.de/forschung/arbeitsgruppe-genominformatik/software/tallymer.html

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