Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data
Open accessAbstract
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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Alignment quality was verified using QualiMap v2.2.1.
“Alignment quality was verified using QualiMap v2.2.155.”
From Integrative genomic analyses identify candidate causal genes for calcific aortic valve stenosis involving tissue-specific regulation (2024) · cites this paper as [55]
Alignment quality was evaluated using Qualimap.
“Alignment quality was evaluated using qualimap (v2.3) [76].”
From Mechanical stiffness orchestrates distinct regulation of <scp>MRTFs</scp> and <scp>YAP</scp> / <scp>TAZ</scp> transcriptional cofactors in hepatocytes (2026) · cites this paper as [76]
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- Authors
- Okonechnikov, K., Conesa, A., & García-Alcalde, F.
- Affiliations
- Max Planck Institute for Infection Biology (DE)
- University of Florida (US)
- Corresponding author
- García-Alcalde, Fernando
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-10-01
- Volume
- 32
- Issue
- 2
- Pages
- 292-294
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC4708105
- OpenAlex
- W2111281047
- Cited by
- 2,145
- References
- 0
- Citations by year
- 2026: 271 · 2025: 295 · 2024: 352 · 2023: 274 · 2022: 267 · 2021: 228 · 2020: 175 · 2019: 114 · 2018: 92 · 2017: 56 · 2016: 20 · 2015: 1
- FWCI
- 24.47
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- HighWire Press Open Archive (submittedVersion)
- Funders
- European Commission (217768)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Keywords
- high-throughput sequencing data, quality control, multi-sample analysis, random error, systematic bias, bioinformatics software
- MeSH terms
- Algorithms, Humans, Quality Control, Software, Sequence Alignment, Sequence Analysis, DNA, Genomics, High-Throughput Nucleotide Sequencing
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