tetano
Editor, Senior Moderator
NAR Genom Bioinform
. 2024 Dec 18;6(4):lqae176.
doi: 10.1093/nargab/lqae176. eCollection 2024 Dec. 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[SUP] 1 2 [/SUP], Finlay Maguire[SUP] 3 4 5 [/SUP], Kendrick M Smith[SUP] 6 [/SUP], Emily M Panousis[SUP] 1 2 [/SUP], Sheridan J C Baker[SUP] 1 2 [/SUP], Patryk Aftanas[SUP] 7 [/SUP], Amogelang R Raphenya[SUP] 1 2 [/SUP], Brian P Alcock[SUP] 1 2 [/SUP], Hassaan Maan[SUP] 8 [/SUP], Natalie C Knox[SUP] 9 10 [/SUP], Arinjay Banerjee[SUP] 1 11 [/SUP], Karen Mossman[SUP] 1 12 13 [/SUP], Bo Wang[SUP] 8 14 15 [/SUP], Jared T Simpson[SUP] 16 17 18 [/SUP], Robert A Kozak[SUP] 7 19 [/SUP], Samira Mubareka[SUP] 7 19 [/SUP], Andrew G McArthur[SUP] 1 2 [/SUP]
Affiliations
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.
. 2024 Dec 18;6(4):lqae176.
doi: 10.1093/nargab/lqae176. eCollection 2024 Dec. 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[SUP] 1 2 [/SUP], Finlay Maguire[SUP] 3 4 5 [/SUP], Kendrick M Smith[SUP] 6 [/SUP], Emily M Panousis[SUP] 1 2 [/SUP], Sheridan J C Baker[SUP] 1 2 [/SUP], Patryk Aftanas[SUP] 7 [/SUP], Amogelang R Raphenya[SUP] 1 2 [/SUP], Brian P Alcock[SUP] 1 2 [/SUP], Hassaan Maan[SUP] 8 [/SUP], Natalie C Knox[SUP] 9 10 [/SUP], Arinjay Banerjee[SUP] 1 11 [/SUP], Karen Mossman[SUP] 1 12 13 [/SUP], Bo Wang[SUP] 8 14 15 [/SUP], Jared T Simpson[SUP] 16 17 18 [/SUP], Robert A Kozak[SUP] 7 19 [/SUP], Samira Mubareka[SUP] 7 19 [/SUP], Andrew G McArthur[SUP] 1 2 [/SUP]
Affiliations
- PMID: 39703420
- PMCID: PMC11655287
- DOI: 10.1093/nargab/lqae176
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.