Figure 2

Simulated contigs, artificial contigs and sequence tags. (a) Generation of simulated contigs and reads from the S. aureus reference sequence. (b) Generation of artificial contigs from assembler output. (c) Tag types. Tags 1 and 2 are a correct join. Tags 2 and 4 demonstrate a skipped tag because the output scaffold jumps over tag 3. Tag 3 also does not appear in the output and is therefore a lost tag. Tags 4 and 5 are in the wrong orientation and tags 5 and 6 belong to different sequences in the reference.