A computerised assignment of genomic sequence values based on multiple reads and probabilistic analysis

摘要

Methods of calling, identifying or assigning genomic sequence values, i.e. nucleotide sequence alignment, in complex calling regions. Complex calling regions which are difficult to match with standard sequence assembler programs. Following a preliminary sequence alignment a complex calling region is identified where no sequence values satisfy preliminary alignment criteria. Potential hypotheses are formulated for the complex calling region and the probability of each hypothesis representing a correct alignment is calculated by evaluating the probability of each hypothesis being correct for the reads and the probability of each hypothesis occurring. The hypothesis best satisfying hypothesis selection criteria is selected. The method may include an evaluation of possible indels in the complex calling region and the preliminary sequence alignment may or may not be based on a reference genome (i.e. may be mapping or comparative assembly or de-novo assembly).