Finished bacterial genomes from shotgun sequence data using ALLPATHS-LG

Our manuscript “Finished bacterial genomes from shotgun sequence data” was just posted as an accepted preprint in Genome Research.  “By applying a new laboratory design and new assembly algorithm to sixteen samples, we demonstrate that assemblies exceeding finished quality can be obtained from whole-genome shotgun data and automated computation.”  Our method is based on assembling a combination of sequence data from Illumina and Pacific Biosciences.  The algorithm is automatically invoked by ALLPATHS-LG when it is supplied with such data, and is already part of the ALLPATHS-LG release.