Abstract: The present invention relates to methods and systems for nucleic acid sequencing. In particular, the present invention relates to methods and systems for reducing the number of false-positives in nucleic acid sequencing. The method comprises: aligning a plurality of genetic reads to a reference genetic sequence; grouping the genetic reads into a plurality of groups; creating a consensus sequence for each group of the plurality of groups by setting a representation of the most abundant nucleotide man_p or a tag N based on a ratio r; and identifying a variation as a true variation if a ratio r* between the number of consensus sequences comprising the tag N at a specific position p and the number of the consensus sequences comprising the variation at the specific position p is below a threshold t*.

Abstract: The present invention relates to a method of identifying structural genomic rearrangements in massively parallel nucleic acid sequencing data, as well as an in vitro method to detect genomic alterations for stratifying patients for cancer therapy, including a step of identifying structural genomic rearrangements. Also provided is a method generating a report including information on the identified.