R-Rsolid-0.9.31-24.fc29 | Build Info

Information for build R-Rsolid-0.9.31-24.fc29

40813

Package Name

R-Rsolid

Version

0.9.31

Release

24.fc29

Epoch

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.

Built by

davidlt

State

complete

Volume

DEFAULT

Started

Fri, 08 Jun 2018 08:38:36 UTC

Completed

Fri, 08 Jun 2018 13:26:25 UTC

Task

build (f29-candidate, R-Rsolid-0.9.31-24.fc29.src.rpm)

Tags

f29

RPMs

src
	R-Rsolid-0.9.31-24.fc29.src.rpm (info) (download)
riscv64
	R-Rsolid-0.9.31-24.fc29.riscv64.rpm (info) (download)
	R-Rsolid-devel-0.9.31-24.fc29.riscv64.rpm (info) (download)
	R-Rsolid-debuginfo-0.9.31-24.fc29.riscv64.rpm (info) (download)
	R-Rsolid-debugsource-0.9.31-24.fc29.riscv64.rpm (info) (download)

Logs

riscv64
	build.log
	hw_info.log
	mock_output.log
	root.log
	state.log

Changelog

* 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 * Wed May 31 2017 Tom Callaway <spot@fedoraproject.org> - 0.9.31-20 - rebuild for R 3.4.0 * Fri Feb 10 2017 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-19 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild * Wed Feb 03 2016 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-18 - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild * Thu Jan 21 2016 Orion Poplawski <orion@cora.nwra.com> - 0.9.31-17 - Rebuild for hdf5 1.8.16 * Tue Jun 16 2015 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-16 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild * Sun May 17 2015 Orion Poplawski <orion@cora.nwra.com> - 0.9.31-15 - Rebuild for hdf5 1.8.15 * Wed Jan 07 2015 Orion Poplawski <orion@cora.nwra.com> - 0.9.31-14 - Rebuild for hdf5 1.8.14 * Fri Aug 15 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild * Fri Jun 06 2014 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild * Fri Aug 02 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild * Thu May 16 2013 Orion Poplawski <orion@cora.nwra.com> - 0.9.31-10 - Rebuild for hdf5 1.8.11 * Fri Apr 12 2013 Tom Callaway <spot@fedoraproject.org> - 0.9.31-9 - rebuild for R3 * Wed Feb 13 2013 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild * Wed Jul 18 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild * Thu Jan 12 2012 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-6 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild * Wed Nov 09 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 * Mon Feb 07 2011 Fedora Release Engineering <rel-eng@lists.fedoraproject.org> - 0.9.31-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild * Mon Aug 23 2010 Adam Huffman <bloch@verdurin.com> - 0.9.31-1 - another upstream bugfix release * Thu Aug 05 2010 Adam Huffman <bloch@verdurin.com> - 0.9.3-1 - New upstream bugfix release * Fri Jul 16 2010 Adam Huffman <bloch@verdurin.com> - 0.9.2-4 - fix duplicated files entries * Fri Jul 16 2010 Adam Huffman <bloch@verdurin.com> - 0.9.2-3 - new upstream release with licensing clarification - specfile cleanups to address reviewer comments: - directory ownership - requires * Mon Jul 12 2010 Adam Huffman <bloch@verdurin.com> - 0.9.2-2 - spec formatting cleanups * Tue Jul 06 2010 Adam Huffman <bloch@verdurin.com> - 0.9.2-1 - new release with ability to disable bundled HDF5 - fix files section - -devel subpackage * Thu Jun 03 2010 Adam Huffman <bloch@verdurin.com> - 0.9.1-1 - initial package for Fedora

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Information for build R-Rsolid-0.9.31-24.fc29