Data science
Efforts to catalog protistan physiological abilities and trophic strategies lag behind those of their prokaryotic counterparts. Interpreting large sequence datasets relies on knowledge gleaned from culture-based transcriptome studies, genetic probing of microorganisms, and single-cell sequencing. We build reproducible pipelines and infrastructure to keep up with growing sequence information.
Check github.com/shu251 for work in process; we are always updating our code.
Sequence analysis workflows
Tag-sequencing
To address questions related to microeukaryotic biodiversity, we use 18S rRNA gene tag-sequencing (also called metabarcoding).
- Tag-sequencing workflow, updated in 2024
- Snakemake implementation for a more robust pipeline
- Building and prepping a database for use in QIIME2
- BVCN resources for amplicon sequencing
Metatranscriptomics
To interrogate in situ microeukaryotic metabolic activity, we target messenger RNA (mRNA) for sequencing through metatranscriptomics.
- Introductory tutorial on metatranscriptomics for eukaryotes
- Extracting microbial eukaryotic information from metagenomes
Lab members contribute to community-wide efforts to examine the range of variability across metatranscriptome bench and computational pipelines, an intercalibration effort funded by OCB: Metaeukomic.
Time-series data
Metabarcoding data are compositional, and we analyze them accordingly. In our R code clubs we emphasize diagnostic steps that confirm the data are being analyzed appropriately.
- Resource for analyzing microbiome time-series data, paired with the publication
- Code from A Hard Day’s Night, which explores temporal niche partitioning among Station ALOHA microeukaryotic communities
Computational tools
Eukaryotic genetics presents computational challenges that prokaryote-focused tools do not solve. We develop tools that automate the assembly, annotation, and processing of meta’omic (metagenome and metatranscriptome) data, and that change how sequence reference databases are queried (see Krinos et al. 2024).
- EUKHeist — code and publication
- EUKulele — documentation and publication
Database Darkly
Deep-sea biodiversity work is limited by the lack of available genetic reference databases. Using results from a large tag-sequencing survey, a team of undergraduate researchers mined biological and ecological information about deep-sea protistan species.
Visit the Database Darkly website to learn more about the microeukaryotes that live in the dark ocean.
Tutorials & teaching
- R code examples and tutorials
- Generating figures from HTS tag-sequencing data, using an OTU or ASV table as input
- Keeping my R life organized — setting up R with conda environments, R, RStudio, and IRKernel
- Learning R with BVCN
New GitHub-hosted tutorial and research sites go here. Add each as a bullet with the site link and a one-line description of what it covers.
- TBD
R packages & side projects
Axial Seamount Wordle
Play our custom Axial Seamount-themed wordle, part of our #protatax expedition.
Woods Hole color palette
Color palettes inspired by Cape Cod and the Woods Hole area, including docks, sunsets, the WHOI logo, and the RV Atlantis. github
ExeRcise
Generate a randomized custom workout. Inspired by high-intensity interval training, the user defines warm-up and workout interval length and the total number of exercises. Additional functions run the workout with a timer in R and generate a tabata-style workout. github
Lab work
Built for personal use only. Functions to streamline molecular bench work and the math required to prepare genetic material for sequencing: PCR master mix calculation, C1V1 = C2V2, and RNA quantification steps. github