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2025
PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance
Bioinformatics
Gabriele Leoni, Mauro Petrillo, Victoria Ruiz-Serra, Maddalena Querci, Sandra Coecke, Tobias Wiesenthal
2024
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
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
2024
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2
F1000Research
Marie Lataretu, Oliver Drechsel, René Kmiecinski, Kathrin Trappe, Martin Hölzer, Stephan Fuchs
2024
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testing and training
Microbial Genomics
Emma J. Griffiths, Inês Mendes, Finlay Maguire, Jennifer L. Guthrie, Bryan A. Wee, Sarah Schmedes, Kathryn Holt, Chanchal Yadav, Rhiannon Cameron, Charlotte Barclay, Damion Dooley, Duncan MacCannell, Leonid Chindelevitch, Ilene Karsch-Mizrachi, Zahra Waheed, Lee Katz, Robert Petit III, Mugdha Dave, Paul Oluniyi, Muhammad Ibtisam Nasar, Amogelang Raphenya, William W. L. Hsiao, Ruth E. Timme
2024
Genome-wide identification and molecular evolution of elongation family of very long chain fatty acids proteins in Cyrtotrachelus buqueti
BMC Genomics
Chun Fu, Ting Yang, Hong Liao, YuLing Huang, HanYu Wang, WenCong Long, Na Jiang, YaoJun Yang
2023
Lessons learned: overcoming common challenges in reconstructing the SARS-CoV-2 genome from short-read sequencing data via CoVpipe2
F1000Research
Marie Lataretu, Oliver Drechsel, René Kmiecinski, Kathrin Trappe, Martin Hölzer, Stephan Fuchs
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