Monthly Archives: July 2012

Finished bacterial genomes from shotgun sequence data using ALLPATHS-LG

Posted on July 25, 2012 by jaffe

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 … Continue reading →

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Chinchilla assembly released

Posted on July 18, 2012 by AllpathsIain

The ALLPATHS-LG assembly of Chinchilla (Chinchilla lanigera) is now available via NCBI and the Broad Institute ftp site. The basic statistics and location are given below: Contig N50 (kb) Scaffold N50 (Mb) NCBI Accession # Broad FTP 61.1 21.9 AGCD00000000 ChiLan1.0 Please read our release terms and … Continue reading →

Posted in Assemblies | Leave a comment

Multi-threading improved

Posted on July 5, 2012 by jaffe

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