Provides a whole‐genome shotgun assembler that can generate high‐quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. The ALLPATHS-LG assemblies are not necessarily linear, but instead are presented in the form of a graph. This graph representation retains ambiguities, such as those arising from polymorphism, uncorrected read errors, and unresolved repeats, thereby providing information that has been absent from previous genome assemblies. ALLPATHS‐LG requires high sequence coverage of the genome in order to compensate for the shortness of the reads. The precise coverage required depends on the length and quality of the paired reads, but typically is of the order 100x or above.