R-Rsolid-0.9.31-41.fc38 | Build Info

Information for build R-Rsolid-0.9.31-41.fc38

233949

Package Name

R-Rsolid

Version

0.9.31

Release

41.fc38

Epoch

Source

git+https://src.fedoraproject.org/rpms/R-Rsolid.git#ccfa79635d9ca1edcb5d6359cab256b1b765b174

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

Mon, 27 Feb 2023 17:49:23 UTC

Completed

Tue, 28 Feb 2023 01:21:52 UTC

Task

build (f38, /rpms/R-Rsolid.git:ccfa79635d9ca1edcb5d6359cab256b1b765b174)

Extra

{'source': {'original_url': 'git+https://src.fedoraproject.org/rpms/R-Rsolid.git#ccfa79635d9ca1edcb5d6359cab256b1b765b174'}}

Tags

f38

RPMs

src
	R-Rsolid-0.9.31-41.fc38.src.rpm (info) (download)
riscv64
	R-Rsolid-0.9.31-41.fc38.riscv64.rpm (info) (download)
	R-Rsolid-devel-0.9.31-41.fc38.riscv64.rpm (info) (download)
	R-Rsolid-debuginfo-0.9.31-41.fc38.riscv64.rpm (info) (download)
	R-Rsolid-debugsource-0.9.31-41.fc38.riscv64.rpm (info) (download)

Logs

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

Changelog

* Wed Jan 18 2023 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-41 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild * Sat Sep 03 2022 Iñaki Úcar <iucar@fedoraproject.org> - 0.9.31-40 - R 4.2.1 * Wed Jul 20 2022 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-39 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild * Wed Jan 19 2022 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-38 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild * Sun Nov 21 2021 Orion Poplawski <orion@nwra.com> - 0.9.31-37 - Rebuild for hdf5 1.12.1 * Tue Aug 10 2021 Orion Poplawski <orion@nwra.com> - 0.9.31-36 - Rebuild for hdf5 1.10.7 * Wed Jul 21 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-35 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild * Mon Jan 25 2021 Fedora Release Engineering <releng@fedoraproject.org> - 0.9.31-34 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild

Main Site Links:

Information for build R-Rsolid-0.9.31-41.fc38