Resources for testing and using the COMPASS Nextflow pipeline. Please see the COMPASS repository for full details.
- Maixner (2021) (FASTQ files used for testing shotgun pipeline)
Frank Maixner, Mohamed S. Sarhan, Kun D. Huang, Adrian Tett, Alexander Schoenafinger, Stefania Zingale, Aitor Blanco-Míguez, Paolo Manghi, Jan Cemper-Kiesslich, Wilfried Rosendahl, Ulrike Kusebauch, Seamus R. Morrone, Michael R. Hoopmann, Omar Rota-Stabelli, Thomas Rattei, Robert L. Moritz, Klaus Oeggl, Nicola Segata, Albert Zink, Hans Reschreiter, Kerstin Kowarik, (2021). Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period. Current Biology, Volume 31, Issue 23, https://doi.org/10.1016/j.cub.2021.09.031.
- Uzan-Yulzari A (2021) (FASTQ files used for testing amplicon pipeline)
Uzan-Yulzari A, Turta O, Belogolovski A, Ziv O, Kunz C, Perschbacher S, Neuman H, Pasolli E, Oz A, Ben-Amram H, Kumar H, Ollila H, Kaljonen A, Isolauri E, Salminen S, Lagström H, Segata N, Sharon I, Louzoun Y, Ensenauer R, Rautava S, Koren O. Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization. Nat Commun. 2021 Jan 26;12(1):443. doi: 10.1038/s41467-020-20495-4. PMID: 33500411; PMCID: PMC7838415.
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Reference databases for testing shotgun pipeline (e.g. Bowtie2 and Kraken2) used courtesy of the Registry of Open Data on AWS. For citation details, please see https://registry.opendata.aws/jhu-indexes/.
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Reference database used for testing shotgun pipeline (Greengenes2 2024.09 training data formatted for DADA2)
Callahan, B. (2024). Greengenes2 training data formatted for DADA2 (Greengenes2 release version 2024.09) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.14169078
McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M. Greengenes2 unifies microbial data in a single reference tree. Nature biotechnology. 2024 May;42(5):715-8.
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nature methods. 2016 Jul;13(7):581-3.