ArticleGenome biology2017
A tandem simulation framework for predicting mapping quality.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Development of Metagenomic Methods for Health Monitoring of Endangered Species Using Fecal Samples.Evolutionary applications · 2026Article
- Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification.Bioinformatics (Oxford, England) · 2025Article
- SigAlign: an alignment algorithm guided by explicit similarity criteria.Nucleic acids research · 2024Article
- Short-read aligner performance in germline variant identification.Bioinformatics (Oxford, England) · 2023Review
- Pathogenic strains ofPeerJ · 2022Article
- Vargas: heuristic-free alignment for assessing linear and graph read aligners.Bioinformatics (Oxford, England) · 2020Article
- Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities.PloS one · 2020Article
- Multimapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone.Proteins · 2020Article
- NGSEP3: accurate variant calling across species and sequencing protocols.Bioinformatics (Oxford, England) · 2019Article
- Joint Estimates of Heterozygosity and Runs of Homozygosity for Modern and Ancient Samples.Genetics · 2019Article
- FORGe: prioritizing variants for graph genomes.Genome biology · 2018Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
Read alignment is the first step in most sequencing data analyses. Because a read's point of origin can be ambiguous, aligners report a mapping quality, which is the probability that the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. I describe a framework for predicting mapping qualities that works by simulating a set of tandem reads. These are like the input reads in important ways, but the true point of origin is known. I implement this method in an accurate and low-overhead tool called Qtip, which is compatible with popular aligners.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.