Figure 1

Idealized assembly graphs [18]of the 5.2 megabase-pair B. anthracis Ames Ancestor main chromosome using (a) 100 bp, (b) 1,000 bp and (c) 5,000 bp reads. The graphs encode the compressed de Bruijn graph derived from infinite coverage error-free reads, effectively representing the repeats in the genome and the upper bound of what could be achieved in a real assembly. Increasing the read length decreases the number of contigs because the longer reads will span more of the repeats. Note the assembly with 5,000 bp reads has a self-edge because the chromosome is circular.