Here we present RedOak, a reference-free and alignment-free software package that allows for the indexing of a large collection of similar genomes. RedOak can also be applied to reads from unassembled genomes, and it provides a nucleotide sequence query function. Our method is about the analysis of complete genomes from the 3000 rice genomes sequencing project, but our indexing structure is generic enough to be used in similar projects. This software is based on a k-mer approach and has been developed to be heavily parallelized and distributed on several nodes of a cluster. The source code of our RedOak algorithm is available at RedOak.