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Information for build R-Rsolid-0.9.31-27.fc31

ID101939
Package NameR-Rsolid
Version0.9.31
Release27.fc31
Epoch
Sourcegit+https://src.fedoraproject.org/rpms/R-Rsolid.git#3622b1e9cbbeeab6e6cd68e538f1b7a6e4a254fd
SummaryQuantile 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.
Built bydavidlt
State failed
Volume DEFAULT
StartedWed, 24 Jul 2019 21:24:46 UTC
CompletedWed, 24 Jul 2019 22:03:20 UTC
Taskbuild (f31-candidate, /rpms/R-Rsolid.git:3622b1e9cbbeeab6e6cd68e538f1b7a6e4a254fd)
Extra{'source': {'original_url': 'git+https://src.fedoraproject.org/rpms/R-Rsolid.git#3622b1e9cbbeeab6e6cd68e538f1b7a6e4a254fd'}}
Tags No tags
RPMs No RPMs
Changelog * Sat Mar 16 2019 Orion Poplawski <orion@nwra.com> - 0.9.31-27 - Rebuild for hdf5 1.10.5 * Thu Jan 31 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-26 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild * Thu Jul 12 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-25 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild * Fri May 18 2018 Tom Callaway <spot@fedoraproject.org> - 0.9.31-24 - rebuild for R 3.5.0 * Wed Feb 07 2018 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-23 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild * Wed Aug 02 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-22 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild * Wed Jul 26 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-21 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild