-------------------------------------------------------------------------------- Fedora Update Notification FEDORA-2011-15950 2011-11-15 23:42:05 --------------------------------------------------------------------------------
Name : R-Rsolid Product : Fedora 15 Version : 0.9.31 Release : 5.fc15 URL : http://rafalab.jhsph.edu/Rsolid/ Summary : Quantile normalization and base calling for second generation sequencing data Description :
Rsolid is an R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles. Under the random DNA fragmentation assumption, these proportions should be equal across sequencing cycles and proportional to the dinucleotide frequencies of the sample.
Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors. Results show that after normalization, the total number of mappable reads increases by around 5%, and number of perfectly mapped reads increases by 10%. Moreover a 2-5% reduction in overall error rates is observed, with a 2-6% reduction in the rate of valid adjacent color mis-matches. The latter is important, since it leads to a decrease in false-positive SNP calls.
The normalization algorithm is computationally efficient. In a test we are able to process 300 million reads in 2 hours using 10 computer cluster nodes. The engine functions of the package are written in C for better performance.
-------------------------------------------------------------------------------- Update Information:
Update R to 2.14.0. This required a mass rebuild of R components. -------------------------------------------------------------------------------- ChangeLog:
* Wed Nov 9 2011 Tom Callaway spot@fedoraproject.org - 0.9.31-5 - rebuild for R 2.14.0 * Thu May 19 2011 Adam Huffman bloch@verdurin.com - 0.9.31-4 - remove executable files to pass check * Tue May 17 2011 Orion Poplawski orion@cora.nwra.com - 0.9.31-3 - Rebuild for hdf5 1.8.7 -------------------------------------------------------------------------------- References:
[ 1 ] Bug #751003 - New version of R 2.14.0 is available https://bugzilla.redhat.com/show_bug.cgi?id=751003 [ 2 ] Bug #753188 - Review Request: R-rtracklayer - R interface to genome browsers and their annotation tracks https://bugzilla.redhat.com/show_bug.cgi?id=753188 [ 3 ] Bug #753181 - Review Request: R-RCurl - General network (HTTP/FTP) client interface for R https://bugzilla.redhat.com/show_bug.cgi?id=753181 [ 4 ] Bug #753182 - Review Request: R-biomaRt - R Interface to BioMart databases https://bugzilla.redhat.com/show_bug.cgi?id=753182 [ 5 ] Bug #753185 - Review Request: R-Rcompression - R Package for in-memory compression https://bugzilla.redhat.com/show_bug.cgi?id=753185 --------------------------------------------------------------------------------
This update can be installed with the "yum" update program. Use su -c 'yum update R-Rsolid' at the command line. For more information, refer to "Managing Software with yum", available at http://docs.fedoraproject.org/yum/.
All packages are signed with the Fedora Project GPG key. More details on the GPG keys used by the Fedora Project can be found at https://fedoraproject.org/keys --------------------------------------------------------------------------------