From Reads to Function Workshop at ISME19
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 ISME19 in Cape Town on August 16 and 17.
- 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
Workshop Agenda
Agendas for each day are listed below. Reminder that the Hybrid Sessions (with webinar components) are only in the morning from 9:00-12:00 local time South Africa.
Reads to Metagenome-Assembled Genomes (MAGs)
South Africa Local Time – Activity / Topic (Lead)
7:45 Travel to Workshop – provided by ISME
8:45 Who is all here?! (Dow)
9:00 Virtual attendees join – Hybrid Session
9:00 Introduction to Workshop and GROW (Borton)
9:20 Introduction to KBase (Allen)
9:50 Break for 10 min
10:00 Introduction to multi-omics methods (Wrighton)
10:25 Assembly QA/QC to Binning (Allen)
10:50 Taxonomic Assessment of Communities (Allen)
11:10 Metagenome-Assembled Genomes (Allen)
11:40 Review and Q&A (Allen)
12:00 End Hybrid Session
Lunch Break
13:00 Workshop Only – Working Session
13:00 Reads to MAGs workflow in KBase (Allen)
14:15 Break for 15 min
14:30 Reads to MAGs workflow in KBase – continued (Allen)
16:00 Report out, recap, and next steps (Allen)
17:00 Depart to hotels
17:30 Networking Event (CoSMic)
MAGs to Function and Metadata Standards
South Africa Local Time – Activity / Topic (Lead) – Activity / Topic (Lead)
7:45 Travel to Workshop provided by ISME
8:30 Review analyses from Day 1 (Allen)
9:00 Virtual attendees join – Hybrid Session
9:00 Microbial Genome Annotation (Borton)
9:30 Metabolism with DRAM (Ellenbogen)
10:00 Break for 15 min
10:15 National Microbiome Data Collaborative (NMDC) and sample metadata (Skoog, Pham, Oduwole)
10:50 DRAM outputs (Borton)
11:00 Publishing with KBase (Dow)
11:30 Q&A, survey (All)
12:00 End Hybrid Session
Lunch Break
13:00 Workshop Only – Working Session
13:00 NMDC sample metadata demonstration (Skoog, Pham, Oduwole)
14:15 Break for 15 min
14:30 Interpreting DRAM (Borton)
16:00 Report out and recap (Borton)
16:45 Close out and survey (Wood-Charlson)
17:00 Depart to hotels
Resources & Helpful Links
Project Paper – in review at Nature
MA Borton, BB McGivern, KR Willi, BJ Woodcroft, AC Mosier, DM Singleton, T Bambakidis, A Pelly, F Liu, JN Edirisinghe, JP Faria, I Leleiwi, RA Daly, AE Goldman, MJ Wilkins, EK Hall, C Pennacchio, S Roux, EA Eloe-Fadrosh, SP Good, MB Sullivan, CS Henry, EM Wood-Charlson, MRV Ross, CS Miller, BC Crump, JC Stegen, KC Wrighton. A functional microbiome catalog crowdsourced from North American rivers. (2023) bioRxiv 2023.07.22.550117; doi: https://doi.org/10.1101/2023.07.22.550117
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
Workshop Activities
Participants from over 50 countries joined the workshop, including 25 individuals who received an Africa Travel Grant from ISME to attend in-person.
Folks also took a Microbe Personality Quiz! Check out the total diversity of our microbial community.
And we compared between our sampling sites – virtual and in-person.
Take the quiz to find out what microbe you are!
People
Colorado State Microbiome Network
Mikayla Borton – Workshop Lead and Microbial Ecosystems Lab co-PI
Jared Ellenbogen – Postdoctoral Researcher, Wrighton Lab
Emily Bechtold – Postdoctoral Researcher, Wilkins Lab
Kelly Wrighton – Microbial Ecosystems Lab PI
KBase
Ben Allen – KBase Outreach Lead
Ellen Dow – KBase Educators Program Lead
Elisha Wood-Charlson – KBase User Engagement Lead
NMDC Ambassadors
Iyanu Oduwole – University of Tennessee – Knoxville
Emilie Skoog – University of California – San Diego, Scripps
Kent Pham – University of Kentucky