Samuel Neuenschwander

A big thank goes to @Ommar_AC and @AnnaSapfo for the great collaboration and @unil, @dbc_unil and @ISBSIB for the support.

In conclusions Centrifuge outperformed the other classifiers. We recommend using strong filters to remove human DNA and to verify if the genomes of interest are included in the classifiers’ database.

Our study «Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study» is out in PeerJ peerj.com/articles/12784/

I would like to thank the coauthors for their support and great work on this project! Yami O. Arizmendi Cárdenas, @MiriamJBravo1, @SamuelNeuensch2, Silvia Reis, @MuriloQBastos, @JesperStenderup, Fulya Eylem Yediay, @VVillaIslas, Carlos S. Reyna-Blanco, [...]

Our study on the genomic history of the Aegean palatial civilizations is out. #aDNA 1/n sciencedirect.com/science/articl…

A big thank to the co-authors YOA Cárdenas and @annasapfo and @UNIL @dbc_unil @ISBSIB for the support.

Centrifuge, Kraken2 and DIAMOND recovered most test viruses while MethPhlAn2 only around one third. While deamination damage has little impact on the performance of the classifiers, DIAMOND and Kraken2 cannot classify very short reads.

Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study biorxiv.org/content/10.110…