title: ABRA: improved coding indel detection via assembly-based realignment.
abstract: BACKGROUND
  Variant detection from next-generation sequencing (NGS) data is an increasingly vital aspect of disease diagnosis, treatment and research. Commonly used NGS-variant analysis tools generally rely on accurately mapped short reads to identify somatic variants and germ-line genotypes. Existing NGS read mappers have difficulty accurately mapping short reads containing complex variation (i.e. more than a single base change), thus making identification of such variants difficult or impossible. Insertions and deletions (indels) in particular have been an area of great difficulty. Indels are frequent and can have substantial impact on function, which makes their detection all the more imperative.
  
  
  RESULTS
  We present ABRA, an assembly-based realigner, which uses an efficient and flexible localized de novo assembly followed by global realignment to more accurately remap reads. This results in enhanced performance for indel detection as well as improved accuracy in variant allele frequency estimation.
  
  
  METHODS
  ABRA is implemented in a combination of Java and C/C++ and is freely available for download at https://github.com/mozack/abra.
authors.affiliation: Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Lisle E
authors.initials: LE
authors.lastname: Mose
authors.affiliation: Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Wilkerson
authors.affiliation: Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: D Neil
authors.initials: DN
authors.lastname: Hayes
authors.affiliation: Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Charles M
authors.initials: CM
authors.lastname: Perou
authors.affiliation: Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, Department of Genetics, Division of Medical Oncology, Department of Internal Medicine, Multidisciplinary Thoracic Oncology Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
authors.forename: Joel S
authors.initials: JS
authors.lastname: Parker
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D005787:Gene Frequency; D015894:Genome, Human; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054643:INDEL Mutation; D011381:Programming Languages; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software