News
VILOCA: sequencing quality-aware viral haplotype reconstruction and mutation calling for short-read and long-read data
We are excited to share that our new tool VILOCA has been published! VILOCA is a novel method for mutation calling and local haplotype reconstruction from diverse viral short-read and long-read sequencing data. It has already proven to be useful in various settings, including classical mutation calling for single or longitudinal samples, and viral surveillance in wastewater. You can check out our published paper in NAR Genomics and Bioinformatics: https://doi.org/10.1093/nargab/lqae152
Release of V-pipe 3.0
We're thrilled to announce the release of V-pipe 3.0! This computational pipeline is specifically crafted for analyzing short viral genomes using next-generation sequencing data. V-pipe 3.0 enables sustainable viral genomic data science. You can check out the published paper on our work in GigaScience at: https://doi.org/10.1093/gigascience/giae065
Assessing different next-generation sequencing technologies for wastewater-based epidemiology
Our paper ‘Assessing different next-generation sequencing technologies for wastewater-based epidemiology’, is now published in Water Research. In this paper we identified tradeoffs in terms of cost, timeliness, and accuracy of wastewater pathogen tracking between different NGS technologies: https://www.sciencedirect.com/science/article/pii/S0043135424013642?via%3Dihub.
The role of bioinformatics in genomic reproducibility
Our review on genomic reproducibility in the bioinformatics era has been published in Genome Biology. The paper provides a comprehensive analysis of how computational methods influence the consistency and accuracy of genomic results, compiling methodologies and datasets for better evaluation of genomic reproducibility.