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AlignerBoost
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AlignerBoost

AlignerBoost is a tool to analyze the mapping of high-throughput sequencing reads and increase the overall mapping precision. It works with all sequence aligners that produce SAM or BAM output and further accepts known SNPs as input to improve the quality of alignments. The authors have specifically optimized AlignerBoost for Bowtie, Bowtie2, NovoAlign, BWA-ALN/BWA-SW/BWA-MEM, SeqAlTo (DNA aligners), and Tophat, Tophat2, STAR (RNA aligners).



AlignerBoost

AlignerBoost is a tool to analyze the mapping of high-throughput sequencing reads and increase the overall mapping precision. It works with all sequence aligners that produce SAM or BAM output and further accepts known SNPs as input to improve the quality of alignments. The authors have specifically optimized AlignerBoost for Bowtie, Bowtie2, NovoAlign, BWA-ALN/BWA-SW/BWA-MEM, SeqAlTo (DNA aligners), and Tophat, Tophat2, STAR (RNA aligners).

Topic

Sequencing

Details

  • Operation: Mapping; Quality affairs
  • Input: SAM, BAM, BED, VCF
  • Output: -
  • Software interface: Command-line user interface
  • Language: Java
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU General Public License v3
    • Cost: Free
  • Version name: 1.8.3
    • Maturity: Stable
  • Credit: The National Institutes of Health, National Institutes of Arthritis and Musculoskeletal and Skin Disease, the National Institute of Nursing Research, Department of Dermatology at University of Pennsylvania.
  • Contact: Qi Zheng zhengqi _at_ mail.med.upenn.edu | Elizabeth A. Grice egrice _at_ mail.med.upenn.edu
  • Collection: -

Publications

Zheng Q, Grice EA "AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework" PLoS Comput Biol. 2016 Oct 5;12(10):e1005096. https://doi.org/10.1371/journal.pcbi.1005096
PMID: 27706155
PMCID: PMC5051939


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