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InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses

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Motivation: InterARTIC is an interactive web application for the analysis of viral whole-genome sequencing (WGS) data generated on Oxford Nanopore Technologies (ONT) devices. A graphical interface enables users with no bioinformatics expertise to analyse WGS experiments and reconstruct consensus genome sequences from individual isolates of viruses, such as SARS-CoV-2. InterARTIC will facilitate the adoption and standardisation of ONT sequencing for viral surveillance and molecular epidemiology.

Worked example: We demonstrate the use of InterARTIC for the analysis of ONT viral WGS data from SARS-CoV-2 and Ebola virus, using a laptop computer or the internal computer on an ONT GridION sequencing device. We showcase the intuitive graphical interface, workflow customization capabilities and job-scheduling system that facilitate execution of small- and large-scale WGS projects on any virus. Implementation & availability: InterARTIC is a free, open-source web application implemented in Python.

The application can be downloaded as a set of pre-compiled binaries that are compatible with all common Ubuntu distributions or built from source. For further details please visit: https://github.com/Psy-Fer/interARTIC/.

Authors: James M Ferguson, Hasindu Gamaarachchi, Thanh Nguyen, Alyne Gollon, Stephanie Tong, Chiara Aquilina-Reid, Rachel Bowen-James, Ira W Deveson
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  • Published on: April 22 2021
  • Source: BioRxiv

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