Foliar fungal symbionts in sympatric yellow monkeyflowers along an elevational gradient in the Sierra Nevada, California, USA
This project aims to explore and characterize the endophytes found oin leaf tissue of Mimulus guttatus, Mimulus laciniatus, Mimulus nasutus and others along an elevational gradient in the Sierra Nevada, California, USA.
The pipeline is mainly focused on the DADA2 pipeline presented by Benjamin Callahan et al. in its ITS and 16S variants. The pipeline follows closely the DADA2 mentioned previously, the work of Mareli Sánchez Juliá for her MAMF project, and Farrer Lab at Tulane University. The USEARCH and VSEARCH steps or alternatives stem from the Arnold Lab at the University of Arizona.
The list below is to help guide your search and aid your bioinformatics journey. Each project and sequencing run is different and should be treated as such. Determine the parameters to filter, cut, trim and truncate accordingly.
- VBL_Bioinformatics folder in the Google Drive were you can find scripts and notes on bioinfomatic pipelines from past graduate students and post-docs.
- Farrer Lab repository. They work on similar data sets.
- DADA2 Main page for the DADA2 workflow. Other links are scattered through the document.
- Callahan, B., McMurdie, P., Rosen, M. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 13, 581–583 (2016).
- Callahan, B., McMurdie, P. & Holmes, S. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J 11, 2639–2643 (2017).
- Bioinformatics Cookbook
Contributions are welcome. Please open an issue or submit a pull request.