Release 41343 includes many changes to the hybrid (Illumina + PacBio) assembly algorithm in ALLPATHS-LG, which result in substantially improved assemblies of bacterial genomes. This completes our work on this problem for now, however we will make changes as needed in response to problems that are reported (if any!).
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.
The ALLPATHS-LG assembly of Spotted Gar (Lepisosteus oculatus) is now available via NCBI and the Broad Institute ftp site. The basic statistics and location are given below:
Please read our release terms and conditions.
The ALLPATHS-LG genome assemblies produced here at the Broad Institute are available for download via the Broad FTP site and NCBI. However, some restrictions on their use may apply, and it is therefore important that you follow the guidelines given below.
All of our assemblies are released under the terms of the Fort Lauderdale Agreement, details of which can be found in the Fort Lauderdale Meeting Report and the associated NHGRI Statement. For some background information and a brief discussion on this agreement, please also read the Nature Editorial on the agreement.
If you would like to use any of the Broad ALLPATHS-LG assemblies listed on this blog in your own research, please first contact the Vertebrate Biology Group by emailing them at email@example.com. Please do not email the ALLPATHS-LG team.
We try very hard to make sure that ALLPATHS-LG is easy to install and use. Over the last year we have noticed that the dependency on the Boost library was the number one cause of installation problems. So we have re-engineered ALLPATHS-LG to remove all the Boost dependencies from the code, and it now no longer requires the Boost libraries to be installed. We hope this will make life easier for you and your sysadmins.