Tools

Meta’omics

• EUKHeist & [preprint] (https://www.biorxiv.org/content/10.1101/2021.07.25.453713v1)

• EUKulele

• Code from a metatranscriptomic survey of protistan trophic strategies

  • EukZoo database, an aquatic protistan protein database for meta-omics studies

Amplicon sequence analysis

• I am currently working on streamlined pipelines to determine Amplicon Sequence Variants (ASVs) or Operational Taxonomic Units (OTUs) using QIIME2 or DADA2 in R for use in environmental microbial ecology.

Data management

• Keeping my R life organized details how I set up R with anaconda on my computer. Introduction to managing projects with conda environments. Includes description of R, RStudio, and IRKernel (jupyter notebooks).

Introduction to R

• R code examples and tutorials

• Generating figures from HTS tag-sequencing data - OTU or ASV table as input

• Learning R with BVCN

Practical Ecology

• Resources for time-series analysis: code and analyses from A Hard Day’s Night

Introduction to tag-sequencing

• QIIME1 or
• QIIME2.
• Also see the BVCN resources for amplicon sequencing

Building reproducible pipeline for amplicon sequence analysis

• Implementing a snakemake workflow to make tag-sequencing pipeline more robust HERE
  • Building/prepping a database for use in QIIME2