Monthly Archives: June 2011

PacBio/Illumina gap patching in ALLPATHS-LG now faster

As of revision 37655, the algorithm that computes the consensus of PacBio reads that patch a gap between ‘Illumina’ contigs is now ~100 times faster. For bacterial genomes it was taking several hours. The speedup was obtained by replacing an … Continue reading

Posted in Release | Leave a comment

Better handling of asymmetric library distributions

The distribution of jumping library fragment (“insert”) sizes can be far from Gaussian. Despite this, assemblers often model these distributions as Gaussian, leading to errors and inaccuracies. As of revision 37618,  ALLPATHS-LG calculates the actual pair separation distribution for all libraries … Continue reading

Posted in Release | Leave a comment

Need Help? Maybe the answer is in our FAQ…

We get many questions from users, but a few keep recurring again and again. We’ve created an FAQ containing answers to these common questions, so perhaps the solution to your particular problem can be already be found here…

Posted in Misc | Leave a comment

Ferret assembly released

The ALLPATHS-LG assembly of female Ferret (Mustela putorius furo) 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 45 9.1 AEYP00000000 MusPutFur1.0 Please read … Continue reading

Posted in Assemblies | Leave a comment