detect SNPs using DNAseq fastq files which were used to assemble the genome

Question

[shl198]

Hello all,

I find a problem that interest me. The chinese hamster genome was assembled using DNAseq. And when I tried to use the same DNAseq to call SNPs, it detected some SNPs. My question is: the assembly should not change the sequence, so there should be no SNPs if I use the same DNAseq which was used to assemble the genome. Does anyone know why this happend? Thanks.

[Ram]

Assuming DNAseq is a k-mer based assembler, the sensitivity during the assembling process is higher than that during SNP calls, which might result in many false positives.