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