From Reads to Function Workshop at ISME Lat 2025
A Workshop on an Accessible Metagenomics Toolkit for Decoding Microbial Contributions to Biogeochemical Cycles
Welcome!
Here you will find the agenda and resources for the From Reads to Function Workshop at the 4th Latin American Congress of Microbial Ecology (ISME Lat 2025), hosted by the Organizing Committee in Mérida, Mexico on August 4 and 5.
- Access to KBase: kbase.us
- Set up a KBase account: https://docs.kbase.us/getting-started/sign-up/step-by-step
- KBase YouTube Channel: http://www.youtube.com/@DOEKBase
- After the introductory webinar and before the workshop, please upload, import & assemble your data.
Workshop Agenda
Agendas for each day below.
Reads to Metagenome-Assembled Genomes (MAGs)
Local Time – Activity / Topic (Lead)
9:00 Lecture: Intro to workshop, GROW, analysis pipeline (Borton & Rodriguez)
9:30 Lecture: Assembly QA/QC to binning in KBase (Dow & Rodriguez)
10:15 Activity: Exploration and evaluation of bin quality
11:00 Lecture: Taxonomic assessment of communities (reads and bins) (Dow & Rodriguez)
11:30 Activity: Explore taxonomic representation
Lunch Break
13:00 Activity: Comparative analysis of community representation
13:30 Report out
13:45 Lecture: Microbial metabolism annotation with DRAM (Borton & Rodriguez)
14:45 Activity: Interpreting microbial metabolism
16:00 Lecture/Activity: NMDC – sample metadata and data portal (Rodriguez)
17:00 Lecture: Publishing with KBase (Dow & Rodriguez)
17:30 Recap, final Q&A, evaluation
18:00 End of Workshop Day 1
Open Office Hours
Local Time – Activity / Topic (Lead)
9:00 Activity: Hands-on work with support & Help Desk (All)
Please have your data assembled and ready to go!
2:00 End of Workshop Day 2
Resources & Helpful Links
Workshop Data and Project Paper
Fadum JM, Borton MA, Daly RA, Wrighton KC, Hall EK. 2024. Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics. mSystems 9:e01059-23. doi: 10.1128/msystems.01059-23
Borton MA, McGivern BB, Willi KR et al. 2025. A functional microbiome catalogue crowdsourced from North American rivers. Nature 637:103–112. doi: 10.1038/s41586-024-08240-z
KBase GROWdb US River Systems Narrative – https://doi.org/10.25982/109073.30/1895615
GROW Org in KBase – https://legacy.narrative.kbase.us/#org/grow
NMDC GROWdb – https://data.microbiomedata.org/details/study/nmdc:sty-11-5tgfr349
People
Colorado State Microbiome Network
Mikayla Borton – Workshop Lead and Microbial Ecosystems Lab co-PI
Kelly Wrighton – Microbial Ecosystems Lab PI
KBase
Ellen Dow – KBase Educators Program Lead
Elisha Wood-Charlson – KBase User Engagement Lead
NMDC Champion
Josue Rodriguez – Postdoctoral Researcher, Pacific Northwest National Laboratory
