Literature DB >> 34908106

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

James M Ferguson1, Hasindu Gamaarachchi1,2, Thanh Nguyen1,2, Alyne Gollon1,2, Stephanie Tong1,2, Chiara Aquilina-Reid1,2, Rachel Bowen-James1,2, Ira W Deveson1,3.   

Abstract

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 is intended to facilitate widespread 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 customisation capabilities and job-scheduling system that facilitate execution of small- and large-scale WGS projects on any common virus. IMPLEMENTATION: InterARTIC is a free, open-source web application implemented in Python that executes best-practice command line workflows from the ARTIC network. The application can be downloaded as a set of pre-compiled binaries that are compatible with all common Linux distributions, Windows with Linux subsystems, MacOSX and ARM systems. For further details please visit: https://github.com/Psy-Fer/interARTIC/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
© The Author(s) 2021. Published by Oxford University Press.

Entities:  

Year:  2021        PMID： 34908106      PMCID： PMC8826086          DOI： 10.1093/bioinformatics/btab846

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  17 in total

1.  Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling.

Authors:  Rebecca J Rockett; Alicia Arnott; Connie Lam; Rosemarie Sadsad; Verlaine Timms; Karen-Ann Gray; John-Sebastian Eden; Sheryl Chang; Mailie Gall; Jenny Draper; Eby M Sim; Nathan L Bachmann; Ian Carter; Kerri Basile; Roy Byun; Matthew V O'Sullivan; Sharon C-A Chen; Susan Maddocks; Tania C Sorrell; Dominic E Dwyer; Edward C Holmes; Jen Kok; Mikhail Prokopenko; Vitali Sintchenko
Journal:  Nat Med       Date:  2020-07-09       Impact factor: 53.440

2.  Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

Authors:  Joshua Quick; Nathan D Grubaugh; Steven T Pullan; Ingra M Claro; Andrew D Smith; Karthik Gangavarapu; Glenn Oliveira; Refugio Robles-Sikisaka; Thomas F Rogers; Nathan A Beutler; Dennis R Burton; Lia Laura Lewis-Ximenez; Jaqueline Goes de Jesus; Marta Giovanetti; Sarah C Hill; Allison Black; Trevor Bedford; Miles W Carroll; Marcio Nunes; Luiz Carlos Alcantara; Ester C Sabino; Sally A Baylis; Nuno R Faria; Matthew Loose; Jared T Simpson; Oliver G Pybus; Kristian G Andersen; Nicholas J Loman
Journal:  Nat Protoc       Date:  2017-05-24       Impact factor: 13.491

3.  Introductions and early spread of SARS-CoV-2 in the New York City area.

Authors:  Ana S Gonzalez-Reiche; Matthew M Hernandez; Emilia Mia Sordillo; Viviana Simon; Harm van Bakel; Mitchell J Sullivan; Brianne Ciferri; Hala Alshammary; Ajay Obla; Shelcie Fabre; Giulio Kleiner; Jose Polanco; Zenab Khan; Bremy Alburquerque; Adriana van de Guchte; Jayeeta Dutta; Nancy Francoeur; Betsaida Salom Melo; Irina Oussenko; Gintaras Deikus; Juan Soto; Shwetha Hara Sridhar; Ying-Chih Wang; Kathryn Twyman; Andrew Kasarskis; Deena R Altman; Melissa Smith; Robert Sebra; Judith Aberg; Florian Krammer; Adolfo García-Sastre; Marta Luksza; Gopi Patel; Alberto Paniz-Mondolfi; Melissa Gitman
Journal:  Science       Date:  2020-05-29       Impact factor: 47.728

4.  Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States.

Authors:  Joseph R Fauver; Mary E Petrone; Emma B Hodcroft; Kayoko Shioda; Hanna Y Ehrlich; Alexander G Watts; Chantal B F Vogels; Anderson F Brito; Tara Alpert; Anthony Muyombwe; Jafar Razeq; Randy Downing; Nagarjuna R Cheemarla; Anne L Wyllie; Chaney C Kalinich; Isabel M Ott; Joshua Quick; Nicholas J Loman; Karla M Neugebauer; Alexander L Greninger; Keith R Jerome; Pavitra Roychoudhury; Hong Xie; Lasata Shrestha; Meei-Li Huang; Virginia E Pitzer; Akiko Iwasaki; Saad B Omer; Kamran Khan; Isaac I Bogoch; Richard A Martinello; Ellen F Foxman; Marie L Landry; Richard A Neher; Albert I Ko; Nathan D Grubaugh
Journal:  Cell       Date:  2020-05-07       Impact factor: 41.582

5.  Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia.

Authors:  Samuel C B Stubbs; Barbara A Blacklaws; Benediktus Yohan; Frilasita A Yudhaputri; Rahma F Hayati; Brian Schwem; Edsel M Salvaña; Raul V Destura; James S Lester; Khin S Myint; R Tedjo Sasmono; Simon D W Frost
Journal:  Virol J       Date:  2020-02-13       Impact factor: 4.099

6.  Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK.

Authors:  Louis du Plessis; John T McCrone; Alexander E Zarebski; Verity Hill; Christopher Ruis; Moritz U G Kraemer; Andrew Rambaut; Oliver G Pybus; Bernardo Gutierrez; Jayna Raghwani; Jordan Ashworth; Rachel Colquhoun; Thomas R Connor; Nuno R Faria; Ben Jackson; Nicholas J Loman; Áine O'Toole; Samuel M Nicholls; Kris V Parag; Emily Scher; Tetyana I Vasylyeva; Erik M Volz; Alexander Watts; Isaac I Bogoch; Kamran Khan; David M Aanensen
Journal:  Science       Date:  2021-01-08       Impact factor: 47.728

7.  Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity.

Authors:  Wilfredo F Garcia-Beltran; Evan C Lam; Kerri St Denis; Adam D Nitido; Zeidy H Garcia; Blake M Hauser; Jared Feldman; Maia N Pavlovic; David J Gregory; Mark C Poznansky; Alex Sigal; Aaron G Schmidt; A John Iafrate; Vivek Naranbhai; Alejandro B Balazs
Journal:  Cell       Date:  2021-04-29       Impact factor: 41.582

8.  Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China.

Authors:  Jing Lu; Louis du Plessis; Zhe Liu; Verity Hill; Min Kang; Huifang Lin; Jiufeng Sun; Sarah François; Moritz U G Kraemer; Nuno R Faria; John T McCrone; Jinju Peng; Qianling Xiong; Runyu Yuan; Lilian Zeng; Pingping Zhou; Chumin Liang; Lina Yi; Jun Liu; Jianpeng Xiao; Jianxiong Hu; Tao Liu; Wenjun Ma; Wei Li; Juan Su; Huanying Zheng; Bo Peng; Shisong Fang; Wenzhe Su; Kuibiao Li; Ruilin Sun; Ru Bai; Xi Tang; Minfeng Liang; Josh Quick; Tie Song; Andrew Rambaut; Nick Loman; Jayna Raghwani; Oliver G Pybus; Changwen Ke
Journal:  Cell       Date:  2020-04-30       Impact factor: 41.582

9.  A genomics network established to respond rapidly to public health threats in South Africa.

Authors:  Nokukhanya Msomi; Koleka Mlisana; Tulio de Oliveira
Journal:  Lancet Microbe       Date:  2020-08-18

10.  Real-time, portable genome sequencing for Ebola surveillance.

Authors:  Joshua Quick; Nicholas J Loman; Sophie Duraffour; Jared T Simpson; Ettore Severi; Lauren Cowley; Joseph Akoi Bore; Raymond Koundouno; Gytis Dudas; Amy Mikhail; Nobila Ouédraogo; Babak Afrough; Amadou Bah; Jonathan Hj Baum; Beate Becker-Ziaja; Jan-Peter Boettcher; Mar Cabeza-Cabrerizo; Alvaro Camino-Sanchez; Lisa L Carter; Juiliane Doerrbecker; Theresa Enkirch; Isabel Graciela García Dorival; Nicole Hetzelt; Julia Hinzmann; Tobias Holm; Liana Eleni Kafetzopoulou; Michel Koropogui; Abigail Kosgey; Eeva Kuisma; Christopher H Logue; Antonio Mazzarelli; Sarah Meisel; Marc Mertens; Janine Michel; Didier Ngabo; Katja Nitzsche; Elisa Pallash; Livia Victoria Patrono; Jasmine Portmann; Johanna Gabriella Repits; Natasha Yasmin Rickett; Andrea Sachse; Katrin Singethan; Inês Vitoriano; Rahel L Yemanaberhan; Elsa G Zekeng; Racine Trina; Alexander Bello; Amadou Alpha Sall; Ousmane Faye; Oumar Faye; N'Faly Magassouba; Cecelia V Williams; Victoria Amburgey; Linda Winona; Emily Davis; Jon Gerlach; Franck Washington; Vanessa Monteil; Marine Jourdain; Marion Bererd; Alimou Camara; Hermann Somlare; Abdoulaye Camara; Marianne Gerard; Guillaume Bado; Bernard Baillet; Déborah Delaune; Koumpingnin Yacouba Nebie; Abdoulaye Diarra; Yacouba Savane; Raymond Bernard Pallawo; Giovanna Jaramillo Gutierrez; Natacha Milhano; Isabelle Roger; Christopher J Williams; Facinet Yattara; Kuiama Lewandowski; Jamie Taylor; Philip Rachwal; Daniel Turner; Georgios Pollakis; Julian A Hiscox; David A Matthews; Matthew K O'Shea; Andrew McD Johnston; Duncan Wilson; Emma Hutley; Erasmus Smit; Antonino Di Caro; Roman Woelfel; Kilian Stoecker; Erna Fleischmann; Martin Gabriel; Simon A Weller; Lamine Koivogui; Boubacar Diallo; Sakoba Keita; Andrew Rambaut; Pierre Formenty; Stephan Gunther; Miles W Carroll
Journal:  Nature       Date:  2016-02-03       Impact factor: 69.504
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  2 in total

1.  poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing.

Authors:  Christian Brandt; Sebastian Krautwurst; Riccardo Spott; Mara Lohde; Mateusz Jundzill; Mike Marquet; Martin Hölzer
Journal:  Front Genet       Date:  2021-07-28       Impact factor: 4.599

2.  A Novel High-Throughput Nanopore-Sequencing-Based Strategy for Rapid and Automated S-Protein Typing of SARS-CoV-2 Variants.

Authors:  Gabriel E Wagner; Massimo G Totaro; André Volland; Michaela Lipp; Sabine Saiger; Sabine Lichtenegger; Patrick Forstner; Dorothee von Laer; Gustav Oberdorfer; Ivo Steinmetz
Journal:  Viruses       Date:  2021-12-19       Impact factor: 5.048
  2 in total

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