SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes
Date
2024-12
Authors
Nasir, Jalees A.
Maguire, Finlay
Smith, Kendrick M.
Panousis, Emily M.
Baker, Sheridan J. C.
Aftana, Patryk
Raphenya, Amogelang R.
Alcock, Brian P.
Maan, Hassaan
Knox, Natalie C.
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford Academic
ORCID
Type
Article
Degree Level
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.
Description
Keywords
SIGNAL, SARS-CoV-2, genomes
Citation
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, 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 Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae176, https://doi.org/10.1093/nargab/lqae176Jalees 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, 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 Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae176, https://doi.org/10.1093/nargab/lqae176
Degree
Department
Program
Advisor
Committee
Part Of
item.page.relation.ispartofseries
DOI
https://doi.org/10.1093/nargab/lqae176