Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples.

de Vries, Jutte; Brown, Julianne; Fischer, Nicole; Sidorov, Igor; Morfopoulou, Sofia; Huang, Jiabin; Munnink, Bas; Sayiner, AYÇA; Bulgurcu, Alihan; Rodriguez, Christophe; Gricourt, Guillaume; Keyaerts, Els; Beller, Leen; Bachofen, Claudia; Kubacki, Jakub; Samuel, Cordey; Florian, Laubscher; Dennis, Schmitz; Beer, Martin; Hoeper, Dirk; Huber, Michael; Kufner, Verena; Zaheri, Maryam; Lebrand, Aitana; Papa, Anna; van Boheemen, Sander; Kroes, Aloys; Breuer, Judith; Xavier Lopez-Labrador, F.; Claas, Eric

doi:10.1016/j.jcv.2021.104908

Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples.

de Vries J. J. C., Brown J. R., Fischer N., Sidorov I. A., Morfopoulou S., Huang J., ...More

Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology, vol.141, pp.104908, 2021 (SCI-Expanded)

Publication Type: Article / Article
Volume: 141
Publication Date: 2021
Doi Number: 10.1016/j.jcv.2021.104908
Journal Name: Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, CAB Abstracts, EMBASE, MEDLINE, Public Affairs Index, Veterinary Science Database
Page Numbers: pp.104908
Keywords: Viral metagenomics, Benchmark, Bioinformatic pipelines, ENCEPHALITIS, ALIGNMENT
Dokuz Eylül University Affiliated: Yes

Abstract

Introduction: Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories.