Almeida et al., 2021
Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., Segata, N., Kyrpides, N. C., and Finn, R. D. (2021).
A unified catalog of 204,938 reference genomes from the human gut microbiome.
Nature Biotechnology, 39(1):105-114.

Anderson, 2001
Anderson, M. (2001).
A new method for non-parametric multivariate analysis of variance.
Austral Ecology, 26(1):32-46.

Callahan et al., 2016
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J., and Holmes, S. P. (2016).
Dada2: High resolution sample inference from illumina amplicon data repository.
Nature Methods, 13:581-583.

Chen et al., 2012
Chen, J., Bittinger, K., Charlson, E. S., Hoffmann, C., Lewis, J., Wu, G. D., Collman, R. G., Bushman, F. D., and Li, H. (2012).
Associating microbiome composition with environmental covariates using generalized unifrac distances.
Bioinformatics, 28(16):2106-13.

Douglas et al., 2020
Douglas, G. M., Maffei, V. J., Zaneveld, J. R., Yurgel, S. N., Brown, J. R., Taylor, C. M., Huttenhower, C., and Langille, M. G. I. (2020).
PICRUSt2 for prediction of metagenome functions.
Nature Biotechnology, 38(6):685-688.

Goodacre et al., 2018
Goodacre, N., Aljanahi, A., Nandakumar, S., Mikailov, M., and Khan, A. S. (2018).
A reference viral database (rvdb) to enhance bioinformatics analysis of high-throughput sequencing for novel virus detection.
MSphere, 3(2):e00069-18.

Hasman et al., 2013
Hasman, H., Saputra, D., Sicheritz-Ponten, T., Lund, O., Svendsen, C. A., Frimodt-Møller, N., and Aarestrup, F. M. (2013).
Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples.
Journal of clinical microbiology, pages JCM-02452.

Kaas et al., 2014
Kaas, R. S., Leekitcharoenphon, P., Aarestrup, F. M., and Lund, O. (2014).
Solving the problem of comparing whole bacterial genomes across different sequencing platforms.

Kaminski et al., 2015
Kaminski, J., Gibson, M. K., Franzosa, E. A., Segata, N., Dantas, G., and Huttenhower, C. (2015).
High-specificity targeted functional profiling in microbial communities with shortbred.
PLoS Comput. Biol.

Kang et al., 2015
Kang, D., Froula, J., Egan, R., and Wang, Z. (2015).
Metabat, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
PeerJ, 3:e1165.

Kelley and Salzberg, 2010
Kelley, D. and Salzberg, S. (2010).
Clustering metagenomic sequences with interpolated markov models.
BMC Bioinformatics, 11:544.

Larsen et al., 2014
Larsen, M. V., Cosentino, S., Lukjancenko, O., Saputra, D., Rasmussen, S., Hasman, H., Sicheritz-Pontén, T., Aarestrup, F. M., Ussery, D. W., and Lund, O. (2014).
Benchmarking of methods for genomic taxonomy.
Journal of clinical microbiology, 52(5):1529-1539.

Narayan et al., 2020
Narayan, N. R., Weinmaier, T., Laserna-Mendieta, E. J., Claesson, M. J., Shanahan, F., Dabbagh, K., Iwai, S., and DeSantis, T. Z. (2020).
Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences.
BMC Genomics, 21(1):56.

Sedlar et al., 2017
Sedlar, K., Kupkova, K., and Provaznik, I. (2017).
Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics.
Computational Structural Biotechnology Journal, 15:48-55.

Ye and Doak, 2009
Ye, Y. and Doak, T. G. (2009).
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes.
PLoS Computational Biology, 5(8):e1000465.

Zankari et al., 2017
Zankari, E., Allesï¿12e, R., Joensen, K. G., Cavaco, L. M., Lund, O., and Aarestrup, F. M. (2017).
Pointfinder: a novel web tool for wgs-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens.
Journal of Antimicrobial Chemotherapy, 72(10):2764-68.