R-Rsolid-0.9.31-25.fc30 | Build Info

Information for build R-Rsolid-0.9.31-25.fc30

82877

Package Name

R-Rsolid

Version

0.9.31

Release

25.fc30

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

Sat, 08 Dec 2018 09:03:21 UTC

Completed

Sat, 08 Dec 2018 11:50:03 UTC

Task

build (f30-candidate, R-Rsolid-0.9.31-25.fc30.src.rpm)

Tags

f30

f31

RPMs

src
	R-Rsolid-0.9.31-25.fc30.src.rpm (info) (download)
riscv64
	R-Rsolid-0.9.31-25.fc30.riscv64.rpm (info) (download)
	R-Rsolid-devel-0.9.31-25.fc30.riscv64.rpm (info) (download)
	R-Rsolid-debuginfo-0.9.31-25.fc30.riscv64.rpm (info) (download)
	R-Rsolid-debugsource-0.9.31-25.fc30.riscv64.rpm (info) (download)

Logs

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

Changelog

* 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 * 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

Main Site Links:

Information for build R-Rsolid-0.9.31-25.fc30