-
Recent Posts
Archives
- August 2014
- May 2014
- May 2013
- April 2013
- March 2013
- January 2013
- December 2012
- November 2012
- October 2012
- September 2012
- August 2012
- July 2012
- May 2012
- April 2012
- March 2012
- February 2012
- January 2012
- December 2011
- November 2011
- October 2011
- September 2011
- August 2011
- July 2011
- June 2011
- May 2011
- April 2011
- March 2011
- February 2011
- January 2011
- December 2010
Categories
Meta
Category Archives: Release
GCC 4.7.0 or higher now required to build ALLPATHS-LG
As of release 44849, GCC 4.7.0 (or higher) is now required to build ALLPATHS-LG. We have made this transition in order to benefit from the many exciting new features afforded by the C++11 standard. If you are unable to access the latest … Continue reading
Posted in News, Release
Leave a comment
Stand alone Error Correction now supports paired reads
The error correction script now supports paired end reads. Simply supply two Fastq files (one for each read direction) and the corrected reads will be returned in the same format. In addition, you may also now run the fragment filling code … Continue reading
Posted in News, Release
Leave a comment
Easy stand alone Error Correction
The ALLPATHS-LG fragment read error correction modules are now available for stand alone use outside the full assembly pipeline. You can now easily error correct your own data using our method without running an assembly. Simply supply a Fastq file … Continue reading
Posted in News, Release
Leave a comment
Multi-threading improved
As of revision 42305, ALLPATHS-LG now sets the environment variable MALLOC_PER_THREAD to 1, which causes each thread to do its own memory allocation. This results in a several percent speed-up, and in some cases, a much greater improvement. We anticipate … Continue reading
Posted in Release
Leave a comment
Improvements to ALLPATHS-LG hybrid assembly algorithm
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 … Continue reading
Posted in Release
Leave a comment
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 … Continue reading
Posted in Release
Leave a comment
Bye Bye Boost
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 … Continue reading
Posted in Release
Leave a comment
FixLocal problem solved – new release now available
The most recent build of AllPathsLG contains an obscure bug fix. Several users reported a failure in FixLocal — a segmentation fault — that we had not seen. The problem was traced to the behavior of the pthreads library in … Continue reading
Posted in Release
Leave a comment
Accuracy of ALLPATHS-LG on small genomes further improved
As of revision 38293, we’ve made a series of accuracy improvements to ALLPATHS-LG. Some of these improvements are specific to hybrid (Illumina + PacBio) datasets. Others are not, but are currently invoked only if the assembly size is under 10 … Continue reading
Posted in Release
Leave a comment
ALLPATHS-LG hybrid assembly accuracy improved
As of revision 38088, for ALLPATHS-LG assembly of ‘hybrid’ Illumina/PacBio datasets, we’ve added a new step that uses the Illumina data to ‘clean’ PacBio patches. This step removes nearly all of the errors introduced by the patches.
Posted in Release
Leave a comment