Improved ALLPATHS-LG hybrid assemblies

After months of development, we are excited to announce a major upgrade to ALLPATHS-LG (as of revision 40776). We have switched over to a fundamentally new algorithm for hybrid (short + long read) assembly of small genomes. The algorithm uses the long reads at a much earlier point in the assembly process and is thus able to better exploit the data.  On our test cases, the new algorithm yields dramatically improved results. We are continuing to work on this new method, so expect to see even more improvements over the coming months. Please note that this upgrade only affects hybrid assemblies, and that currently only bacterial sized genomes can be assembled in this manner.