METHOD AND DEVICE FOR IDENTIFYING EXTENSION CONFLICT AND DETERMINING CONFIDENCE LEVEL OF SEED READ IN NUCLEOTIDE SEQUENCE ASSEMBLY

摘要

Disclosed is a method for identifying extension conflict and determining a confidence level of a seed read in nucleotide sequence assembly. The method comprises: selecting, from reads for gap closure, all reads that overlap one end of a first contig close to a gap and taking the all reads as a gap closure read set, and selecting, from the gap closure read set, a read having the shortest overlap as a seed read; determining whether the gap closure read set has a read having the length of an overlap with the first contig being shorter than the length of an overlap between the seed read and the first contig, and whether the gap closure read set has a read that does not overlap the seed read; if any one of the two determination results is yes, indicating that extension conflict occurs, and determine that the seed read is inconvincible; reselecting a convincible seed read, and splicing the seed read and the first contig, so as to perform the gap closure. Further disclosed is an apparatus for identifying extension conflict and determining a confidence level of a seed read in nucleotide sequence assembly.