A method for finding associated positions of bases of a read on a reference genome.

摘要

The invention relates to a method for finding associated positions of bases of a read on a reference genome. Each base has a position number on the read. The method comprises a procedure to obtain P sequence parts of the read. The procedure comprises a first loop to obtain P candidates and extending each of the candidates by preceding and/or following bases of the read to obtain the P sequence parts. A sequence part matches a part of the reference genome according to predefined criteria at a location on the reference genome. The first loop to obtain the P candidates comprises the actions: determining the number of locations on the reference genome which perfectly matches a partial sequence with a length of M bases from the read, the partial sequence starting at a base with position number S; and, repeating the previous action by increasing the value of M as long as the number of locations on the reference genome which perfectly matches is larger than a predefined number T, where P ≤ T.