Increasing read length is viewed as the crucial condition for fragment assembly with next-generation sequencing technologies. However, introducing mate-paired reads (separated by a gap of length GapLength) opens a possibility to transform short mate-pairs into long mate-reads of length approximately GapLength, and thus raises the question as to whether the read length (as opposed to GapLength) even matters. We introduce Paired de Bruijn graphs that address this issue and provide an attractive alternative to a traditional de Bruijn assembly assembly used in existing NGS tools. We further describe recent advances in single cell DNA sequencing and demonstrate that with appropriate assembly tools, the quality of bacterial single cell sequencing may approach the quality of traditional multicell sequencing. We further show how our approach to DNA sequencing can be generalized to Shotgun Protein Sequencing (SPS). We illustrate applications of SPS to sequencing of snake venoms and antibodies and show how mass-spectrometry enables de novo sequencing of peptide-like antibiotics.