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A tandem simulation framework for predicting mapping quality.

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.

SUBMITTER: Langmead B

PROVIDER: S-EPMC5557537 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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A tandem simulation framework for predicting mapping quality.

Langmead Ben B

Genome biology 20170810 1

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 orig ...[more]

PMID: 28806977

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