Gustaf: generic multi-split alignment finder

Abstract

Large-scale population and disease association studies have shown the importance as well as the difficulty of detecting structural variants (SVs) in genomic and also transcriptomic sequencing data. Although being very fast and precise, current read mapping tools usually fail to map sequencing reads that cross SV breakpoints or exon-exon boundaries. These events cause one or even multiple splits in the read-to-reference alignment, with parts of the read mapping to various locations on the reference sequence. We present GUSTAF [1], a sound generic multi-split detection method implemented in the C++ library SeqAn [4]. GUSTAF uses SeqAn’s exact local aligner Stellar [2] to find partial read alignments, and reports precise breakpoints of SVs and exon-exon boundaries.