Next-generation sequencing technology is enabling massive production of high-quality paired-end reads. Many platforms (Illumina Genome Analyzer, Applied Biosystems SOLID, Helicos HeliScope) are currently able to produce "ultra-short" paired reads of lengths starting at 25 nt. An analysis by Whiteford et al. [1] on sequencing using unpaired reads shows that ultra-short reads theoretically allow whole genome re-sequencing and de novo assembly of only small eukaryotic genomes. By conducting an analysis extending Whiteford et al. results, we investigate to what extent genome re-sequencing is feasible with ultra-short paired reads. We obtain theoretical read length lower bounds for re-sequencing that are also applicable to paired-end de novo assembly.