SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes

Jalees A Nasir; Finlay Maguire; Kendrick M Smith; Emily M Panousis; Sheridan J C Baker; Patryk Aftanas; Amogelang R Raphenya; Brian P Alcock; Hassaan Maan; Natalie C Knox; Arinjay Banerjee; Karen Mossman; Bo Wang; Jared T Simpson; Robert A Kozak; Samira Mubareka; Andrew G McArthur

doi:10.1093/nargab/lqae176

SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes

NAR Genom Bioinform. 2024 Dec 18;6(4):lqae176. doi: 10.1093/nargab/lqae176. eCollection 2024 Dec.

Authors

Jalees A Nasir^{1

2}, Finlay Maguire^{3

4

5}, Kendrick M Smith⁶, Emily M Panousis^{1

2}, Sheridan J C Baker^{1

2}, Patryk Aftanas⁷, Amogelang R Raphenya^{1

2}, Brian P Alcock^{1

2}, Hassaan Maan⁸, Natalie C Knox^{9

10}, Arinjay Banerjee^{1

11}, Karen Mossman^{1

12

13}, Bo Wang^{8

14

15}, Jared T Simpson^{16

17

18}, Robert A Kozak^{7

19}, Samira Mubareka^{7

19}, Andrew G McArthur^{1

2}

Affiliations

¹ M.G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.
² Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.
³ Faculty of Computer Science, Dalhousie University, 6050 University Avenue, Halifax, Nova Scotia, B3H 1W5, Canada.
⁴ Institute for Comparative Genomics, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada.
⁵ Department of Community Health & Epidemiology, Dalhousie University, 5790 University Avenue, Halifax, Nova Scotia, B3H 1V7, Canada.
⁶ Perimeter Institute for Theoretical Physics, 31 Caroline Street North, Waterloo, Ontario, N2L 2Y5, Canada.
⁷ Division of Microbiology, Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, 2075 Bayview Avenue, Toronto, Ontario, M4N 3M5, Canada.
⁸ Peter Munk Cardiac Centre, University Health Network, 585 University Avenue, Toronto, Ontario, M5G 2N2, Canada.
⁹ National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3G 1G1, Canada.
¹⁰ Department of Medical Microbiology and Infectious Diseases, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, Manitoba, R3E 0J9, Canada.
¹¹ Department of Veterinary Microbiology, Vaccine and Infectious Disease Organization, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan, S7N 5E3, Canada.
¹² Department of Medicine, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.
¹³ McMaster Immunology Research Centre, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4K1, Canada.
¹⁴ Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7, Canada.
¹⁵ Vector Institute for Artificial Intelligence, 661 University Avenue, Toronto, Ontario, M5G 1M1, Canada.
¹⁶ Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Ontario, M5G 0A3, Canada.
¹⁷ Department of Computer Science, University of Toronto, 40 St George Street, Toronto, Ontario, M5S 2E4, Canada.
¹⁸ Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
¹⁹ Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.

Abstract

The incorporation of sequencing technologies in frontline and public health healthcare settings was vital in developing virus surveillance programs during the Coronavirus Disease 2019 (COVID-19) pandemic caused by transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, increased data acquisition poses challenges for both rapid and accurate analyses. To overcome these hurdles, we developed the SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL) for quick bulk analyses of Illumina short-read sequencing data. SIGNAL is a Snakemake workflow that seamlessly manages parallel tasks to process large volumes of sequencing data. A series of outputs are generated, including consensus genomes, variant calls, lineage assessments and identified variants of concern (VOCs). Compared to other existing SARS-CoV-2 sequencing workflows, SIGNAL is one of the fastest-performing analysis tools while maintaining high accuracy. The source code is publicly available (github.com/jaleezyy/covid-19-signal) and is optimized to run on various systems, with software compatibility and resource management all handled within the workflow. Overall, SIGNAL illustrated its capacity for high-volume analyses through several contributions to publicly funded government public health surveillance programs and can be a valuable tool for continuing SARS-CoV-2 Illumina sequencing efforts and will inform the development of similar strategies for rapid viral sequence assessment.