As the genomic data generated by high throughput sequencing machines continue to exponentially grow, the need for very efficient bioinformatics tools to extract relevant knowledge from this mass of data doesn't weaken. Comparing sequences is still a major task in this discovering process, but tends to be more and more time-consuming. KLAST is a sequence comparison software optimized to compare two nucleotides or proteins data sets, typically a set of query sequences and a reference bank. Performances of KLAST are obtained by a new indexing scheme, an optimized seed-extend methodology, and a multi-level parallelism implementation. To scale up to NGS data processing, a Hadoop version has been designed. Experiments demonstrate a good scalability and a large speed-up over BLAST, the reference software of the domain. In addition, computation can be optionally performed on compressed data without any loss in performances.