-
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: News
DISCOVAR de novo now available
We are pleased to announce the release of DISCOVAR de novo, our new assembler that is suitable suitable for large genomes up to human size. DISCOVAR de novo, uses the same cheap data that the original DISCOVAR release does: 250 base paired-end … Continue reading
Posted in News
Leave a comment
DISCOVAR is here!
The ALLPATHS-LG team have been busy lately working on a new project: DISCOVAR is both a genome assembler and a variant caller. It requires only a single Illumina fragment library to run, leading to cheaper genome assemblies and low cost … Continue reading
Posted in News
Leave a comment
Assessing assembly methods
For purposes of assessing our assembly methods, we generated some NA12878 clone reference sequences. We believe that these data will be of interest to the community and have therefore decided to make them available to all. These clone sequences and the … Continue reading
Posted in Misc, News
Leave a comment
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
FASTG specification released
The FASTG Format Specification Working Group is pleased to announce version 1.0 of the FASTG specification FASTG is a format for faithfully representing genome assemblies in the face of allelic polymorphism and assembly uncertainty. Currently genome assemblies are represented linearly, … Continue reading
Posted in News
Leave a comment
Transitioning to community support for ALLPATHS-LG
Over the past two years we have provided direct support to ALLPATHS-LG users. We believe this has been valuable to all, including us, as it has allowed us to improve our product — making it easier to install and use, … Continue reading
Posted in News
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
Bacterial example data now available
Don’t have any suitable data yet, but would still like to try out ALLPATHS-LG? In support of our recent hybrid assembly paper, we have provided data suitable for both Illumina only and Illumina + Pacific Biosciences bacterial assemblies. For something larger you … Continue reading
Posted in News
Leave a comment
Broad Institute to offer genome sequencing and assembly service for bacterial genomes.
The Broad Institute is preparing to offer a service that takes as input a bacterial DNA sample and provides as output a genome assembly based on the new laboratory and computational methods. For further information please write to AssemblyService@broadinstitute.org.
Posted in News
Leave a comment