Next-generation sequencing technologies are currently wellestablished in the research field and progressively find their way towards clinical applications. Sequencers produce vast amounts of data and therefore bioinformatics methods are needed for processing. Without computational methods, sequencing would not be able to produce relevant biological information. In this review, we introduce the basics of common NGSrelated bioinformatics methods used in oncological research. We also state some of the common problems complicating data processing and interpretation of the results.Key words: bioinformatics - highthroughput nucleotide sequencing - mutations - cancer research - clinical applicationThis study was supported by the European Regional Development Fund and the State Budget of the Czech Republic (RECAMO, CZ.1.05/2.1.00/03.0101), by the project MEYS – NPS I – LO1413, MH CZ – DRO (MMCI, 00209805) and BBMRI_CZ (LM2010004).The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study.The Editorial Board declares that the manuscript met the ICMJE “uniform requirements” for biomedical papers.Submitted: 21. 4. 2015Accepted: 26. 6. 2015.