Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk.

The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging.

Unfazed: parent-of-origin detection for large and small de novo variants.

Summary: Unfazed is a command-line tool to determine the parental gamete of origin for de novo mutations from paired-end Illumina DNA sequencing reads. Unfazed uses variant information for a sequenced trio to identify the parental gamete of origin by linking phase-informative inherited variants to de novo mutations using read-based phasing. It achieves a high success rate by chaining reads into haplotype groups, thus increasing the search space for informative sites.

Samplot: a platform for structural variant visual validation and automated filtering.

Visual validation is an important step to minimize false-positive predictions from structural variant (SV) detection. We present Samplot, a tool for creating images that display the read depth and sequence alignments necessary to adjudicate purported SVs across samples and sequencing technologies. These images can be rapidly reviewed to curate large SV call sets.

Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data.

The rapid increase in the amount of genomic data provides researchers with an opportunity to integrate diverse datasets and annotations when addressing a wide range of biological questions. However, genomic datasets are deposited on different platforms and are stored in numerous formats from multiple genome builds, which complicates the task of collecting, annotating, transforming, and integrating data as needed. Here, we developed Go Get Data (GGD) as a fast, reproducible approach to installing standardized data recipes.

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families.

Each human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity, they can also create deleterious alleles that impact fitness. Whereas the rate and patterns of point mutations in the human germline are now well understood, far less is known about the frequency and features that impact de novo structural variants (dnSVs).

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data.

Ribosome profiling, an application of nucleic acid sequencing for monitoring ribosome activity, has revolutionized our understanding of protein translation dynamics. This technique has been available for a decade, yet the current state and standardization of publicly available computational tools for these data is bleak. We introduce XPRESSyourself, an analytical toolkit that eliminates barriers and bottlenecks associated with this specialized data type by filling gaps in the computational toolset for both experts and non-experts of ribosome profiling.

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants.

SV-plaudit is a framework for rapidly curating structural variant (SV) predictions. For each SV, we generate an image that visualizes the coverage and alignment signals from a set of samples. Images are uploaded to our cloud framework where users assess the quality of each image using a client-side web application.