Stephen Turner

nf-core/genomeqc: a best-practice pipeline for comparing genome and assembly quality

The paper introduces a pipeline for assessing and comparing genome assembly quality using multiple metrics and tools.

Survey and Evaluation of Applied Containerization Practices in Bioinformatics

The paper evaluates containerization practices in bioinformatics, finding that most containers fail to build or pull, with version control activity predicting success.

Single-cell and spatial transcriptomics of the avian embryo tailbud

The paper generates a molecular map of the avian trunk and tailbud using single-cell and spatial transcriptomics, identifying cell lineages and spatially restricted genes.

tfboot: Bootstrapping and statistical analysis for transcription factor binding site-disrupting variants in gene sets

The paper introduces tfboot, an R package for statistically evaluating TFBS disruption in gene sets using bootstrapping methods.

Internal Validation of the ForenSeq Kintelligence Kit for Application to Forensic Genetic Genealogy

The paper validates the ForenSeq Kintelligence kit for forensic genetic genealogy, demonstrating reliable SNP profiles from low-input and degraded samples.

k2v: A Containerized Workflow for Creating VCF Files from Kintelligence Targeted Sequencing Data

k2v converts Kintelligence sequencing data into VCF files, enabling use of existing tools for genetic analysis.

Developmental Validation of the Illumina Infinium Assay using the Global Screening Array (GSA) on the iScan System for use in Forensic Laboratories

This study validates the Illumina Infinium assay using the Global Screening Array (GSA) for forensic applications according to SWGDAM guidelines, showing high SNP call rates and sample quality assessment methods.

vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework

vcferr simulates SNP genotyping errors in VCF files to assess their impact on kinship analysis.

Environmental DNA sequencing data from algal blooms in Lake Erie using Oxford Nanopore MinION

The paper describes a portable sequencing pipeline for detecting harmful algal blooms using environmental DNA from Lake Erie, showing significant differences in HAB-associated taxa abundance before and after a bloom.

skater: An R package for SNP-based Kinship Analysis, Testing, and Evaluation

The paper introduces the skater R package for SNP-based kinship analysis, testing, and evaluation, providing tools for pedigree data handling and relationship degree inference.

The maternal-fetal interface of successful pregnancies and impact of fetal sex using single cell sequencing

The paper uses single-cell RNA sequencing to analyze maternal-fetal interface cell types and identifies sex-specific differences in immune cell function and regulatory pathways.