ABRA

ABRA performs assembly-based realignment of next-generation sequencing (NGS) reads to improve alignment accuracy and enhance detection and variant allele frequency estimation of complex variants such as insertions and deletions (indels).

Key Features:

• Localized De Novo Assembly: Employs localized de novo assembly to reconstruct sequences from reads that contain complex variations.
• Global Realignment: Performs global realignment of reconstructed sequences to the reference genome to improve mapping accuracy.
• Improved Indel Detection: Combines localized assembly and global realignment to enhance detection of insertions and deletions (indels).
• Accurate Variant Allele Frequency Estimation: Improves accuracy of variant allele frequency estimation from aligned reads.

Scientific Applications:

• Disease Diagnosis and Treatment: Improves detection of somatic variants and germline genotypes relevant to diagnosis and personalized treatment planning.
• Genomic Research: Enables analysis of complex genomic variation and supports studies of genetic diversity and evolution.

Methodology:

Implemented in Java and C/C++; methodology comprises localized de novo assembly of reads followed by global realignment of reconstructed sequences to the reference genome.