Large biological datasets are being produced at a rapid pace and create substantial storage challenges, particularly in the domain of high-throughput sequencing (HTS). Most approaches currently used to store HTS data are either unable to quickly adapt to the requirements of new sequencing or analysis methods (because they do not support schema evolution), or fail to provide state of the art com...

High-throughput sequencing has drastically changed the research of genes responsible for genetic disorders and is now gradually introduced as an additional genetic diagnostic testing in clinical practice. The current debates on the emerging technical, medical and ethical issues as well as the potential optimum use of the available technology are discussed.

The DNA in our cells contains our genetic hereditary information, and is literally the blueprint of our body. The functional units of the genome are regions of continuous DNA sequence, and are called genes. According to the Central Dogma of Biology, the DNA sequence of the gene is transcribed into a messenger RNA (mRNA), which is in turn translated to proteins, which perform most tasks in the c...

High-throughput genomic technology has enabled us to screen the entire genome and generate hypotheses at relatively low costs. One of the driving forces in highthroughput genomic technology is high-throughput sequencing (HTS).With its rapid development and affordability, HTS has quickly become the go-to choice for interrogating the entire genome. The analysis methodology development for HTS has...

We show that existing RNA-seq, DNase-seq, and ChIP-seq data exhibit overdispersed per-base read count distributions that are not matched to existing computational method assumptions. To compensate for this overdispersion we introduce a nonparametric and universal method for processing per-base sequencing read count data called FIXSEQ. We demonstrate that FIXSEQ substantially improves the perfor...

Next-generation sequencing technologies are now common for whole-genome, whole-exome and whole-transcriptome sequencing (RNA-seq) of tumors to identify point mutations, structural or copy number alterations and changes in gene expression. A substantial number of studies have already been performed for melanoma. One study analysed eight melanoma cell lines with RNA-Seq technology and identified ...

Background: Nonsense-mediated mRNA decay (NMD) affects the outcome of alternative splicing by degrading mRNA isoforms with premature termination codons. Splicing regulators constitute important NMD targets; however, the extent to which loss of NMD causes extensive deregulation of alternative splicing has not previously been assayed in a global, unbiased manner. Here, we combine mouse genetics a...

The distinction between model and nonmodel organisms is becoming increasingly blurred. High-throughput, second-generation sequencing approaches are being applied to organisms based on their interesting ecological, physiological, developmental, or evolutionary properties and not on the depth of genetic information available for them. Here, we illustrate this point using a low-cost, efficient tec...

MOTIVATION A ubiquitous and fundamental step in high-throughput sequencing analysis is the alignment (mapping) of the generated reads to a reference sequence. To accomplish this task, numerous software tools have been proposed. Determining the mappers that are most suitable for a specific application is not trivial. RESULTS This survey focuses on classifying mappers through a wide number of c...