AlignerBoost – A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or “best” hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present.

Researchers from the University of Pennsylvania School of Medicine have developed a generalized software toolkit “AlignerBoost”, which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. They tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer.

The mapping sensitivity vs. False Discovery Rate (FDR) curves under different mapping quality (mapQ) cutoffs for the simulated RNA-seq datasets


The mapQ varies from 0, 3, 6, 10, 13, 20, then in increments of 10 up to the maximum allowed values of the indicated aligner. “Default” indicates aligners’ default best hits; “AlignerBoost” indicates best hits via AlignerBoost mapping and filtering procedures. A: Single-end (SE) mapping; B: Paired-end (PE) mapping.

Availability – AlignerBoost is implemented as a uniform Java application and is freely available at

Zheng Q, Grice EA. (2016) AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework. PLoS Comput Biol 12(10):e1005096. [article]

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