Qualimap 2: Advanced Multi-sample Quality Control for High-throughput Sequencing Data

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2015 Oct 3

PMID 26428292

Citations 913

Authors

Konstantin Okonechnikov

Ana Conesa

Fernando Garcia-Alcalde

Affiliations

Soon will be listed here.

Abstract

Motivation: Detection of random errors and systematic biases is a crucial step of a robust pipeline for processing high-throughput sequencing (HTS) data. Bioinformatics software tools capable of performing this task are available, either for general analysis of HTS data or targeted to a specific sequencing technology. However, most of the existing QC instruments only allow processing of one sample at a time.

Results: Qualimap 2 represents a next step in the QC analysis of HTS data. Along with comprehensive single-sample analysis of alignment data, it includes new modes that allow simultaneous processing and comparison of multiple samples. As with the first version, the new features are available via both graphical and command line interface. Additionally, it includes a large number of improvements proposed by the user community.

Availability And Implementation: The implementation of the software along with documentation is freely available at http://www.qualimap.org.

Contact: meyer@mpiib-berlin.mpg.de

Supplementary Information: Supplementary data are available at Bioinformatics online.

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References

DeLuca D, Levin J, Sivachenko A, Fennell T, Nazaire M, Williams C . RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012; 28(11):1530-2. PMC: 3356847. DOI: 10.1093/bioinformatics/bts196. View

Patel R, Jain M . NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012; 7(2):e30619. PMC: 3270013. DOI: 10.1371/journal.pone.0030619. View

Koeppel M, Garcia-Alcalde F, Glowinski F, Schlaermann P, Meyer T . Helicobacter pylori Infection Causes Characteristic DNA Damage Patterns in Human Cells. Cell Rep. 2015; 11(11):1703-13. DOI: 10.1016/j.celrep.2015.05.030. View

Anders S, McCarthy D, Chen Y, Okoniewski M, Smyth G, Huber W . Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat Protoc. 2013; 8(9):1765-86. DOI: 10.1038/nprot.2013.099. View

Ross M, Russ C, Costello M, Hollinger A, Lennon N, Hegarty R . Characterizing and measuring bias in sequence data. Genome Biol. 2013; 14(5):R51. PMC: 4053816. DOI: 10.1186/gb-2013-14-5-r51. View

Sims D, Sudbery I, Ilott N, Heger A, Ponting C . Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014; 15(2):121-32. DOI: 10.1038/nrg3642. View

Rosenbloom K, Sloan C, Malladi V, Dreszer T, Learned K, Kirkup V . ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2012; 41(Database issue):D56-63. PMC: 3531152. DOI: 10.1093/nar/gks1172. View

Adams D, Altucci L, Antonarakis S, Ballesteros J, Beck S, Bird A . BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol. 2012; 30(3):224-6. DOI: 10.1038/nbt.2153. View

Wang L, Wang S, Li W . RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012; 28(16):2184-5. DOI: 10.1093/bioinformatics/bts356. View

10.

Garcia-Alcalde F, Okonechnikov K, Carbonell J, Cruz L, Gotz S, Tarazona S . Qualimap: evaluating next-generation sequencing alignment data. Bioinformatics. 2012; 28(20):2678-9. DOI: 10.1093/bioinformatics/bts503. View

11.

Ramirez-Gonzalez R, Leggett R, Waite D, Thanki A, Drou N, Caccamo M . StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics. F1000Res. 2014; 2:248. PMC: 3938176. DOI: 10.12688/f1000research.2-248.v2. View