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Kraken

A universal genomic coordinate translator for comparative genomics

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Methods

Article - BMC Bioinformatics


Overview

Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings.


Getting started

Download the package, unzip and run make from the main directory. Use gcc version 4.2 or higher for this. You can start by running the code with the data provided in the samples directory. This is explained below.



Example The following example performs a mapping of items in the GTF input file "dmel.gtf" from specie "dmel" to "dyak". The data for this example can be found in the sample folder. The output is written to mapped.gtf as default. You can run the command: ../runKraken -c dere_dyak_dmel.config -s dmel.gtf -S dmel -T dyak


For more information, see the software guide located in the repository (doc/softwareGuide.pdf)