Read alignment is an ongoing challenge for the analysis of data from sequencing
technologies. This article proposes an elegantly simple multi-seed strategy, called seed-and …

Motivation: Discovering variation among high-throughput sequenced genomes relies on
efficient and effective mapping of sequence reads. The speed, sensitivity and accuracy of …

With the introduction of next-generation sequencing (NGS) technologies, we are facing an
exponential increase in the amount of genomic sequence data. The success of all medical …

The recent introduction of new DNA sequencing techniques caused the amount of
processed and stored biological data to skyrocket. In order to process these vast amounts of …

Genome analysis is becoming more important in the fields of forensic science, medicine,
and history. Sequencing technologies such as High Throughput Sequencing (HTS) and …

In this paper, we describe our vision to accelerate algorithms in the domain of genomic data
analysis by proposing a framework called Genesis (genome analysis) that contains an …

Sequence alignment is a fundamental operation in genomic analysis where DNA fragments
called reads are mapped to a long reference DNA sequence. There exist a number of (in) …

Innovations in genome sequencing techniques are enabling remarkably fast and low cost
production of raw genome data. As Moore's law tapers off, bottlenecks in genome …

We present our work on hardware accelerated genomics pipelines, using either FPGAs or
GPUs to accelerate execution of BWA-MEM, a widely-used algorithm for genomic short read …

Background As the next-generation sequencing (NGS) technologies producing hundreds of
millions of reads every day, a tremendous computational challenge is to map NGS reads to …