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., ...Daha Fazla

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

Yayın Türü: Makale / Tam Makale
Cilt numarası: 141
Basım Tarihi: 2021
Doi Numarası: 10.1016/j.jcv.2021.104908
Dergi Adı: Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology
Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, CAB Abstracts, EMBASE, MEDLINE, Public Affairs Index, Veterinary Science Database
Sayfa Sayıları: ss.104908
Anahtar Kelimeler: Viral metagenomics, Benchmark, Bioinformatic pipelines
Dokuz Eylül Üniversitesi Adresli: Evet

Özet

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.