Aligning sequencing reads onto a reference is an essential step of the majority of genomic
analysis pipelines. Computational algorithms for read alignment have evolved in …

Structural variations (SVs) are mutations in the genome of size at least fifty nucleotides. They
contribute to the phenotypic differences among healthy individuals, cause severe diseases …

A key goal of whole-genome sequencing for studies of human genetics is to interrogate all
forms of variation, including single-nucleotide variants, small insertion or deletion (indel) …

Large structural variations (SVs) within genomes are more challenging to identify than
smaller genetic variants but may substantially contribute to phenotypic diversity and …

Although great progress has been made in the characterization of the off-target effects of
engineered nucleases, sensitive and unbiased genome-wide methods for the detection of …

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data,
and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble …

Comprehensive discovery of structural variation (SV) from whole genome sequencing data
requires multiple detection signals including read-pair, split-read, read-depth and prior …

Unbiased, high-throughput assays for detecting and quantifying DNA double-stranded
breaks (DSBs) across the genome in mammalian cells will facilitate basic studies of the …

Variation in the presence or absence of transposable elements (TEs) is a major source of
genetic variation between individuals. Here, we identified 23,095 TE presence/absence …

It has been over a decade since the first publication of a method dedicated entirely to
mapping long-reads. The distinctive characteristics of long reads resulted in methods …