Scripts used for sequencing data handling

manuscript in prep by Ate H. Jaarsma

ampvis.R

creating heatmaps + Venn diagrams

Andersen, Kasper S., Rasmus H. Kirkegaard, Soren M. Karst, and Mads Albertsen. 2018. “Ampvis2: An r Package to Analyse and Visualise 16s rRNA Amplicon Data.” bioRxiv. https://doi.org/10.1101/299537.

metacoder.R

creating heat trees + alpha diversity measures

Foster, Zachary, Thomas Sharpton, and Niklaus Grünwald. 2017. “Metacoder: An r Package for Visualization and Manipulation of Community Taxonomic Diversity Data.” PLOS Computational Biology 13 (2): 1–15. https://doi.org/10.1371/journal.pcbi.1005404.

Qiime2_16S_18S.txt

amplicon data analysis

Bolyen E, Rideout JR, Dillon MR et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 2019 378 2019;37:852–7.