Sunday, June 16th - 2 Hour - Afternoon - 3:00 pm - 5:00 pm

Fees, where indicated, include coffee breaks and any necessary supplies

Sold Out - Genome Skimming: A Bioinformatics Approach to Assembly-Free Analysis of Genomic Information

Organized by: Eduardo Charvel

Traditional Cyanotype Printing with Jessie Swimeley

Organized by: Jessie Swimeley

Ethnobotany, natural products, and microbiomes through a One Health collaboration

Organized by: Matthew Kolp


Workshop Descriptions

Genome Skimming: A Bioinformatics Approach to Assembly-Free Analysis of Genomic Information

Submitted By:  Eduardo Charvel


Genome skimming (low-coverage shotgun-sequencing) approaches to evolution and population genetics offer flexible alternatives to traditional methods left to DNA (meta)barcoding, bypassing the need for PCR amplification of marker regions or by avoiding computationally expensive processes of assembly alignment (Bohmann et al. 2020). As the cost of shotgun-sequencing keeps decreasing, the potential use for these skimming methods in the study of genomic ecology is higher than ever. In this workshop, we will be looking at a low-coverage sequencing analysis pipeline with a variety of functions, including decontamination, genomic distance inference, phylogenetic placement, and estimation genome repetitiveness. The pipeline consists of a set of user-friendly command-line tools dedicated to analyzing low-coverage genome skims (

Firstly we will be talking about CONSULT-II: a taxonomic identification tool that extracts k-mers from a query read and classifies them against k-mers in a reference database. In the context of the pipeline, we will be using it to remove reads that classify as bacterial contaminants, keeping reads that are specific to our organism of interest (Şapcı et al. 2022).

We will also be discussing Skmer, an alignment-free tool that estimates distances between genomes by looking at how many shared k-mers are found between sequences and outputs a distance matrix which you can use to create a phylogenetic tree (Sarmashghi et al 2019).

With a reference tree constructed by distance matrix generated from Skmer, we then use another tool APPLES for fast, alignment-free phylogenetic placement (Balaban et al 2020).

Finally, we will talk about RESPECT, a tool to accurately estimate properties like repetitiveness, genome length, sequencing coverage and error (Sarmashghi et al 2021).

This workshop will cover installation instructions, an overview discussion of how the methods function, and applying the suite of tools in your local computer and/or cluster. The workshop will work through a tutorial analyzing a small plant genome dataset.

Planned Speakers

Eduardo Charvel, UC San Diego
Siavash Mirarab, UC San Diego

Traditional Cyanotype Printing with Jessie Swimeley

Submitted By:  Jessie Swimeley


Create Traditional Cyanotype prints with artist, Jessie Swimeley. Learn the history, chemistry, and artistry of this historic photographic contact printing process. Traditional Cyanotype printing and botany have a long history of making beautiful blue works of art together!
Bring fresh or pressed samples of your favorite botanicals to use to create your artwork. Plants with strong silhouettes work the best, but we can definitely try anything!

Planned Speakers

Jessie Swimeley

Ethnobotany, natural products, and microbiomes through a One Health collaboration

Submitted By:  Matthew Kolp


Join us to draw your focus back to the fundamentals of collaboration across disciplines, a core concept of One Health research. In this 2-hour workshop, we will discuss and invite discussion from participants on productive, collaborative behavior in their fields. Then we will present our research in ethnobotany: how do native plants of Appalachia and their derived natural products compare for the purported medicinal, immunological, and phytopathogenic effects? How do plant endophytes and microbiome members contribute to these traits? We present our methods including but not limited to the application of HPTLC, mass spectrometry, and microbiome analyses; we also share our preliminary findings. We end our workshop with an outline of a review paper on Plant Microbiomes and Appalachian Folk Medicine and invite workshop participants to join as authors.

This workshop is for:
• Researchers and students at any stage of their career with no, some, or lots of expertise in topic areas (ethnobotany, plant endophytes, natural products, HPTLC and mass spec)
• Those interested in discussing the fundamentals of successful, productive, and collaborative behavior.
• Those interested in ethnobotany, phytopharmacology, plant chemistry, and/or endophytes.
• Those interested in collaborating with us to produce a One Health review paper on the intersection of ethnobotany, natural products, and microbiomes.

Folks that attend our workshop will:
• Create a list of productive, collaborative behavior to use in their research.
• Discuss their experiences of successful collaborative behavior.
• Gain knowledge of ethnobotany of Appalachia, the significance of natural products research, and plant endophytes as an abundant source of bioactive compounds.
• Consider committing to a collaboration with our group to produce a review paper and conduct empirical research on plant endophytes of ethnobotanically important natural products.


Matthew Kolp, Lincoln Memorial University, Richard A. Gillespie College of Veterinary Medicine
Marybeth Babos, Lincoln Memorial University, DeBusk College of Osteopathic Medicine
Noel Cawley, Lincoln Memorial University, School of Mathematics and Sciences, Cumberland Mountain Research Center
Lori McGrew, Lincoln Memorial University, DeBusk College of Osteopathic Medicine