The tremdendous advances in high-throughput sequencing technologies have made
population-scale sequencing as performed in the 1000 Genomes project and the
Genome of the Netherlands project possible. Next-generation sequencing has
allowed genom-wide discovery of variations beyond single-nucleotide
polymorphisms (SNPs), in particular of structural variations (SVs) like
deletions, insertions, duplications, translocations, inversions, and even more
complex rearrangements. Here, we design a read aligner with special emphasis on
the following properties: (1) high sensitivity, i.e. find all (reasonable)
alignments; (2) ability to find (long) indels; (3) statistically sound
alignment scores; and (4) runtime fast enough to be applied to whole genome
data. We compare performance to BWA, bowtie2, stampy and find that our methods
is especially advantageous on reads containing larger indels
