R-Rsolid-0.9.31-30.fc33 | Build Info

Information for build R-Rsolid-0.9.31-30.fc33

148872

Package Name

R-Rsolid

Version

0.9.31

Release

30.fc33

Epoch

Source

git+https://src.fedoraproject.org/rpms/R-Rsolid.git#1fcc1b582fad9de9a4f400e844aacb9df1af024f

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, 27 Mar 2020 18:31:16 UTC

Completed

Fri, 27 Mar 2020 19:36:32 UTC

Task

build (f33, /rpms/R-Rsolid.git:1fcc1b582fad9de9a4f400e844aacb9df1af024f)

Extra

{'source': {'original_url': 'git+https://src.fedoraproject.org/rpms/R-Rsolid.git#1fcc1b582fad9de9a4f400e844aacb9df1af024f'}}

Tags

f33

RPMs

src
	R-Rsolid-0.9.31-30.fc33.src.rpm (info) (download)
riscv64
	R-Rsolid-0.9.31-30.fc33.riscv64.rpm (info) (download)
	R-Rsolid-devel-0.9.31-30.fc33.riscv64.rpm (info) (download)
	R-Rsolid-debuginfo-0.9.31-30.fc33.riscv64.rpm (info) (download)
	R-Rsolid-debugsource-0.9.31-30.fc33.riscv64.rpm (info) (download)

Logs

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

Changelog

* Tue Jan 28 2020 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-30 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild * Mon Aug 12 2019 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 0.9.31-29 - Remove explicit dependencies provided by automatic dependency generator * Wed Jul 24 2019 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-28 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild * 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

Main Site Links:

Information for build R-Rsolid-0.9.31-30.fc33