Highlights•Analysis of massive NGS datasets poses difficult computational challenges.•Big
data algorithms are often adapted for NGS analysis.•HPC becomes pivotal as NGS …

Read mapping is a fundamental step in many genomics applications. It is used to identify
potential matches and differences between fragments (called reads) of a sequenced …

Over the past decade, short-read sequence alignment has become a mature technology.
Optimized algorithms, careful software engineering and high-speed hardware have …

Read mapping is a fundamental, yet computationally-expensive step in many genomics
applications. It is used to identify potential matches and differences between fragments …

Ultra-high-throughput next-generation sequencing (NGS) technology allows us to determine
the sequence of nucleotides of many millions of DNA molecules in parallel. Accompanied by …

Nanopore sequencing is a widely-used high-throughput genome sequencing technology
that can sequence long fragments of a genome into raw electrical signals at low cost …

Memory bandwidth and latency constitutes a major performance bottleneck for many data-
intensive applications. While high-locality access patterns take advantage of the deep cache …

In heterozygous genomes, allele-specific measurements can reveal biologically significant
differences in DNA methylation between homologous alleles associated with local changes …

Motivation Read alignment is an essential first step in the characterization of DNA sequence
variation. The accuracy of variant-calling results depends not only on the quality of read …

The rise of data-intensive algorithms, such as Machine Learning ones, has meant a strong
diversification of Graphics Processing Units (GPU) in fields with intensive Data-Level …