Simplified model showing how fragment-to-fragment concatenations can be generated. DNA polymerase can create overhangs during PCR amplification. An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule (e.g. a single adenosine as a 3'-overhang). The unpaired nucleotides are removed to generate blunt-ended DNA molecules with both strands terminating in a base pair. This step can produce fragment-to-fragment concatenations because blunt ends are compatible with each other. The 454 adaptors are added to the amplified fragments by blunt-end ligation before sequencing. The resulting sequence data can contain artificial concatenated sequences.
Schmieder et al. BMC Bioinformatics 2010 11:341 doi:10.1186/1471-2105-11-341