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An alignment-free method and associated program to compute relative absent words (RAW) in genomic sequences using a reference sequence. Currently, EAGLE runs on a command line linux environment, building an image with patterns reporting the absent words regions (in SVG) as well as reporting the associated positions into a file. EAGLE has got scripts to run on the current outbreak and the other existing ebola virus genomes (using the human as a reference), including the download, filtering and processing of the entire data.
A command line tool for generating, for a given reference genome, a set of k-mers absent in that genome. The main differences with respect to previously developed tools for neverwords generation are (i) calculation of the distance from the reference genome, in terms of number of mismatches, and selection of the most distant sequences that will have a low probability to anneal unspecifically; (ii) application of a series of filters to discard candidates not suitable to be used as PCR primers.
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