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Monthly Archives: July 2011
Long read patching is now even easier
Using long reads for patching is now fully integrated into the ALLPATHS-LG pipeline – manual data preparation is no longer required. Please download the latest release (37843 or above) and the accompanying manual that describes how to incorporate long reads into your … Continue reading
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ALLPATHS-LG much faster with Transparent Huge Pages
Starting with version 2.6.38, the Linux kernel allows for Transparent Huge Pages (THP), a mechanism whereby memory pages of size 2MB are used in ‘situations where they would be useful’, rather than the standard 4KB pages. We have found that … Continue reading
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Stringency of long read patches increased
ALLPATHS-LG will patch gaps in scaffolds using long reads from PacBio. As of revision 37660 we have tightened up the join process so that long reads having longer overlaps with their neighboring contigs are given more weight. This leads to … Continue reading
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