SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes DOI Creative Commons
Jalees A. Nasir, Finlay Maguire, Kendrick M. Smith

и другие.

NAR Genomics and Bioinformatics, Год журнала: 2024, Номер 6(4)

Опубликована: Сен. 28, 2024

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

Язык: Английский

Diphyllin elicits a doubled-pronged attack on the entry of SARS-CoV-2 by inhibiting cathepsin L and furin DOI Creative Commons

Binli Mao,

Vu Thuy Khanh Le‐Trilling,

Haoran Tang

и другие.

Virus Research, Год журнала: 2024, Номер 350, С. 199485 - 199485

Опубликована: Окт. 19, 2024

Язык: Английский

Процитировано

0
SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes DOI Creative Commons
Jalees A. Nasir, Finlay Maguire, Kendrick M. Smith

и другие.

NAR Genomics and Bioinformatics, Год журнала: 2024, Номер 6(4)

Опубликована: Сен. 28, 2024

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

Язык: Английский

Процитировано

0