ssahaSNP - a polymorphism detection tool on a whole genome scale

We present a software package which can detect homozygous SNPs and indels on a eukaryotic genome scale from millions of shotgun reads. Matching seeds of a few kmer words are found to locate the position of the read on the genome. Full sequence alignment is performed to detect base variations. Quality values of both variation bases and neighbouring bases are checked to exclude possible sequence base errors. To analyze polymorphism level in the genome, we used the package to detect indels from 20 million WGS reads against the draft WGS assembly. From the dataset, we detected a total number of 663,660 indels, giving an estimated average indel density at about one indel every 2.48 kilobases. Distribution of indels length and variation of indel mapped times are also analyzed.