References

Credits & Acknowledgements

The pipeline is based on nf-core’s AmpliSeq pipeline version 2.1.0.

nf-core

Ewels, P., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature biotechnology, 38(3), 276–278. https://doi.org/10.1038/s41587-020-0439-x

AmpliSeq release 2.1.0

Straub, D., Peltzer, A., Lundin, D., Tångrot, J., Emnilsson, DiegoBrambilla, Bot, N.-C., Gabernet, G., PhilPalmer, Garcia, M. U., Davenport, C., Ewels, P., Patel, H., & Menden, K. (2021, September 14). NF-core/ampliseq: Ampliseq version 2.1.0 “gray steel boa”. https://doi.org/10.5281/zenodo.5506988

AmpliSeq introduction paper

Straub, D., Blackwell, N., Langarica-Fuentes, A., Peltzer, A., Nahnsen, S., & Kleindienst, S. (2020). Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. Frontiers in microbiology, 11. https://doi.org/10.3389/fmicb.2020.550420 PMID: 33193131; PMCID: PMC7645116.

Tools & Assets

Nextflow

Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316–319. https://doi.org/10.1038/nbt.3820. PubMed PMID: 28398311.

FastQC

Andrews, S. (2019). A Quality Control tool for High Throughput Sequence Data. Babraham Bioinformatics. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Cutadapt

Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1). https://doi.org/10.14806/ej.17.1.200

DADA2

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13(7). https://doi.org/10.1038/nmeth.3869

SILVA database

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2013). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41(D1). https://doi.org/10.1093/nar/gks1219

QIIME2

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E.J., Arumugam, M., Asnicar, F., Bai, Y., Bisanz, J. E., Bittinger, K., Brejnrod, A., Brislawn, C. J., Brown, C. T., Callahan, B. J., Caraballo-Rodríguez, A. M., Chase, J., Cope, E. K., Da Silva, R., Diener, C., Dorrestein, P. C., Douglas, G. M., Durall, D. M., Duvallet, C., Edwardson, C. F., Ernst, M. , Estaki, M., Fouquier, J., Gauglitz, J. M., Gibbons, S. M., Gibson, D. L., Gonzalez, A., Gorlick, K., Guo, J., Hillmann, B., Holmes, S., Holste, H., Huttenhower, C., Huttley, G. A., Janssen, S., Jarmusch, A. K., Jiang, L., Kaehler, B. D., Kang, K. B., Keefe, C. R., Keim, P., Kelley, S.T., Knights, D., Koester, I., Kosciolek, T., Kreps, J., Langille, M. G. I., Lee, J., Ley, R., Liu, Y. X., Loftfield, E., Lozupone, C., Maher, M., Marotz, C., Martin, B. D., McDonald, D., McIver, L. J., Melnik, A. V., Metcalf, J. L., Morgan, S. C., Morton, J. T., Naimey, A. T., Navas-Molina, J. A., Nothias, L. F., Orchanian, S. B., Pearson, T., Peoples, S. L., Petras, D., Preuss, M. L., Pruesse, E., Rasmussen, L. B., Rivers, A., Robeson, M. S., Rosenthal, P., Segata, N., Shaffer, M., Shiffer, A., Sinha, R., Song, S. J., Spear, J. R., Swafford, A. D., Thompson, L. R., Torres, P. J., Trinh, P., Tripathi, A., Turnbaugh, P. J., Ul-Hasan, S., van der Hooft, J. J. J., Vargas, F., Vázquez-Baeza, Y., Vogtmann, E., von Hippel, M., Walters, W., Wan, Y., Wang, M., Warren, J., Weber, K. C., Williamson, C. H. D, Willis A. D., Xu, Z. Z., Zaneveld, J. R., Zhang, Y., Zhu, Q., Knight, R., & Caporaso, J. G. (2019). Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature Biotechnology, 37(8). https://doi.org/10.1038/s41587-019-0209-9

MultiQC

Ewels, P., & Magnusson, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Oxford Academic Bioinformatics, 32(19). https://doi.org/10.1093/bioinformatics/btw354

KronaTools

Ondov, B. D., Bergman, N. H., & Phillippy, A. M. (2011). Interactive metagenomic visualization in a Web browser. BMC bioinformatics, 12, 385. https://doi.org/10.1186/1471-2105-12-385