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| Sala, Claudia; Mordhorst, Hanne; Grützke, Joesphine; Brinkmann, Annika; Petersen, Thomas N; Poulsen, Casper; Cotter, Paul D; Crispie, Fiona; Ellis, Richard J; Castellani, Gastone; Amid, Clara; Hakhverdyan, Mikhayil; Le Guyader, Soizick; Manfreda, Gerardo; Mossong, Joël; Nitsche, Andreas; Ragimbeau, Catherine; Schaeffer, Julien; Schlundt, Joergen; Tay, Moon Y. F.; Aarestrup, Frank M.; Hendriksen, Rene S.; Pamp, Sünje Johanna; De Cesare, Alessandra. |
| An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members... |
| Tipo: Text |
Palavras-chave: Shotgun metagenomics; Smoked salmon; Proficiency test; Experimentally spiked samples; Wet-lab protocols. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00664/77615/79636.pdf |
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