Introduction

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.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.ABRA is implemented in a combination of Java and C/C++ and is freely available for download at https://github.com/mozack/abra.

Publications

  1. ABRA: improved coding indel detection via assembly-based realignment.
    Cite this
    Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS, 2014-10-01 - Bioinformatics (Oxford, England)

Credits

  1. Lisle E Mose
    Developer

    Lineberger Comprehensive Cancer Center, Department of Genetics, United States of America

  2. Matthew D Wilkerson
    Developer

    Lineberger Comprehensive Cancer Center, Department of Genetics, United States of America

  3. D Neil Hayes
    Developer

    Lineberger Comprehensive Cancer Center, Department of Genetics, United States of America

  4. Charles M Perou
    Developer

    Lineberger Comprehensive Cancer Center, Department of Genetics, United States of America

  5. Joel S Parker
    Investigator

    Lineberger Comprehensive Cancer Center, Department of Genetics, United States of America

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT002605
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC, C++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJoel S Parker