An introduction to V-pipe

Virus populations exist as heterogeneous ensembles of genomes either within hosts in clinical samples or among hosts in environmental samples. V-pipe is a computational pipeline for analyzing virus next-generation sequencing (NGS) data, specializing in samples of mixed viral populations.

Get Started with V-pipe

Meet Us

V-pipe will be present at the Swiss bioinformatics summit 2024

SIB Days 2024

Applying V-pipe to SARS-Coronavirus-2 data

Webinar demonstrating the use of V-pipe, an end-to-end bioinformatics pipeline that integrates various computational tools for the analysis of high-throughput sequencing data, on SARS-Coronavirus-2 samples.

Applying V-pipe

Vpipe featuring VILOCA

VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data

VILOCA is designed to analyze genetically heterogeneous samples. Its tools provide error correction, haplotype reconstruction and estimation of the frequency of the different genetic variants present in a mixed sample.

VILOCA

Vpipe featuring COJAC

CoOccurrence adJusted Analysis and Calling

cojac offers a set of tools to analyze co-occurrence of mutations on amplicons, e.g., for early detection of viral variants of concern in environmental samples such as wastewater samples. doi:10.1038/s41564-022-01185-x

COJAC

Vpipe featuring LolliPop

LolliPop is a tool for Wastewater Genomics for deconvolution of viral variants and estimation of their relative abundance, even in case of shared mutations among variants. It is resilient to noise and overdispersion in the sequencing data, and leverages the time series. doi:10.1101/2022.11.02.22281825

LolliPop