Visualize metagenomic data

Uzon picture

We are reaching out to hear from others what tools they are using to assign and visualize gene functions in environmental samples of microbial communities.


Our dataset is simple. We did a metagenomic analysis of two pools (samples/sites). First, we co-assembled the whole metagenome for each pool. Then, we used anvi’o to bin individual bacterial and archaeal genomes within the pools. These genomes (bins) were then fed into RAST. This online software gives you a table of known genes for each bin. At the moment we have an array of tables with known microbial genes for each pool that we would like to visualize/summarize in an aesthetically pleasing way. We tried to use summary statistics in MG-RAST, but the upload failed eight times in a row (including several attempts of uploading individual bins as fasta files, co-assembled metagenomes as fasta files, and sequence reads before assembly as fastq files). The upload failures were identified as cashing problems or internal errors.


We went back to using anvi’o using NCBI COG assignments, following their infant gut pangenome tutorial ( which in the end gives you a similar output to RAST in tabular format.


What software are people using out there to compare, assign and visualize gene functions across samples and across bins? Can these tabular outputs be used as inputs for any software producing visually pleasing figures?


(The foto is taken from

At #UCDavis 10/5: Rebecca Vega Thurber “Hosts and Habitats: Tracking shifts in animal microbiomes under stress”

Evolution and Ecology Seminar

Rebecca Vega Thurber

Oregon State University

“Hosts and Habitats: Tracking shifts in animal microbiomes under stress ”

Thursday​, ​
October 5​, 2017​

4:10 – 5:30PM
3 Kleiber Hall

See more about her work here:

At #UCDavis today: Rich Corsi Living in a Material World: Why the Surfaces that Surround You Affect What You Breathe

Living in a Material World:

Why the Surfaces that Surround You Affect What You Breathe

Richard L. Corsi, Ph.D., The University of Texas at Austin

Environmental & Water Resources Fall Seminar Series

Tuesday, October 3, 12:10 pm, 3102b Ghausi Hall

From infancy to twilight years, the air that we breathe and surfaces that we touch inside buildings have a substantial impact on our lifetime exposure to air pollution, including pollution of outdoor origin. As such, there is value in understanding the processes that affect the sources and fate of air pollutants indoors, with a goal of manipulating these processes to improve the air that we breathe.

An important feature of indoor atmospheres is the relatively large ratio of surface area to volume of air, particularly in comparison to the same ratio for the outdoor atmosphere. From building materials to architectural coatings, flooring to furniture, and HVAC system components to human occupants, indoor surfaces vary considerably from one another and within and between buildings. These surfaces are sources of air pollutants and reservoirs (sinks) onto and into which pollutants adsorb, absorb and persist. They contain reaction sites that permanently remove pollutants while forming others. They also allow for direct contaminant transfer following physical contact. Importantly, indoor materials and their surfaces are dynamic, with changes that occur over time scales of minutes to decades and that can dramatically influence surface interactions with pollutants in indoor air.

This presentation will begin with a discussion of the importance of indoor air quality, including the broader impacts associated with its improvement and the intellectual merit of its continued study. The importance of indoor materials and their impacts on indoor air quality will be explored using several examples from past and ongoing research that reflect different interfacial phenomena and influencing factors. The potential for smart use of materials for improvement of indoor air quality will also be discussed as a rich topic for future research.

There are materials around you that are affecting the amount and nature of pollutants that you are inhaling as you read this abstract. Get to know them.

Richard L. Corsi is a proud graduate of the Department of Civil and Environmental Engineering at UC Davis (MS 1985, PhD 1989). He is a Distinguished Engineering Alumni Medal recipient of the College of Engineering at UC Davis (2016) and was named a Distinguished Alumnus of Humboldt State University in 2006. Dr. Corsi is past Chair of the Department of Civil, Architectural and Environmental Engineering at the University of Texas at Austin and currently holds the Joe J. King Chair in Engineering. His research focuses on sources, fate, human exposure and innovative control strategies related to indoor air quality. In recent years his team has focused significantly on ozone-initiated chemistry and indoor air quality. He serves as Vice-President of the Academy of Fellows of the International Society of Indoor Air Quality and Climate. In 2015, Dr. Corsi was inducted into the University of Texas Academy of Distinguished Teachers (top 5%), and in 2016 he received a Regents Outstanding Teaching Award from the University of Texas System.

Richard Harris of NPR at #UCDavis 10/25 “Common Errors that Bedevil Biomedical Research and How to Fix Them,”

Got this and am following the instructions:


We are pleased to announce that Dr. Richard Harris, Distinguished Science Writer- NPR Correspondent on Science, Medicine, and the Environment, will be presenting the Storer Lectureship in Life Sciences Series, “Common Errors that Bedevil Biomedical Research and How to Fix Them,” at 4:10 p.m. on Wednesday, October 25, 2017 in the Student Community Center, Multipurpose Room. Please see the attached flyer for additional information. Richard will be signing his book, “Rigor Mortis- How Sloppy Science creates Worthless Cures, Crushes Hope and Wastes Billions, ” immediately after the lecture.

Richard Harris_flyer fnl.pdf

At #UCDavis 10/3 Taichi Suzuki “The interplay between host genetics and the gut microbiome in wild mice”

CPB Seminar Reminder for Tuesday, October 3, 4:10pm in 1022 Life Sciences

Speaker: Taichi Suzuki

Graduate Student, Nachman Lab, UC Berkeley

Title: The interplay between host genetics and the gut microbiome in wild mice

Host: Katie Ferris,

Call for applications: UC President’s Postdoctoral Fellowship Program

Attached is the 2018-19 Call for Applications for the UC President’s Postdoctoral Fellowship Program awards.

Please feel free to forward the attached call for applications to your professional networks that include:

Graduate students;

PhD candidates;

Postdoctoral appointees;

Department/Division chairs; and

Campus Diversity Officers.

The application deadline is November 1, 2017.

University of California



THE PROGRAM. The University of California President’s Postdoctoral Fellowship Program was established in 1984 to encourage outstanding women and minority Ph.D. recipients to pursue academic careers at the University of California. The current program offers postdoctoral research fellowships and faculty mentoring to outstanding scholars in all fields whose research, teaching, and service will contribute to the diversity and equal opportunity at the University of California. The contributions to diversity may include public service towards increasing equitable access in fields where women and minorities are underrepresented. In some fields, the contributions may include research focusing on underserved populations or understanding inequalities related to race, gender, disability or LGBT. The program is seeking applicants with the potential to bring to their academic and research careers the critical perspective that comes from their non‐traditional educational background or understanding of the experiences of members of groups historically underrepresented in higher education in the United States.

AWARDS AND APPOINTMENTS. Fellowships are awarded for research conducted at any one of the University of California’s ten campuses.

The award includes a salary starting at approximately $48,200 depending on field and experience, benefits including health insurance and paid vacation/sick leave, and up to $5,000 for research‐related and program travel expenses. Each award is for a minimum of 12‐months and may be renewable for an additional term upon demonstration of academic/research productivity.

ELIGIBILITY. Applicants must receive a Ph.D. from an accredited university before the start of their fellowship. Successful applicants must present documents demonstrating that they are legally authorized to work in the United States. Individuals granted deferred action status under the Deferred Action for Childhood Arrivals program are encouraged to apply.

Apply online at:

DEADLINE: November 1, 2017


Los Angeles
San Diego
San Francisco
Santa Barbara
Santa Cruz

More information:
President’s Postdoctoral Fellowship Program University of California visit online:
email: ppfpinfo

University Partnerships for Faculty Diversity

Partner Programs with University of Minnesota, Carnegie Mellon University, University of Colorado, Boulder, University of Maryland, University of Michigan, The California Alliance, UC Chancellor’s Postdoctoral Fellowship Programs, and the UC‐affiliated National Labs.
Please visit:

2018-19 Call for Applications.pdf

Publishing Symposia at #UCDavis Main Campus and Med School, October 16 & 17

The Office of Research, the UC Davis Library, and the UC Davis Clinical and Translational Science Center at the School of Medicine are hosting two Publishing Symposia.
The UC Davis campus Publishing Symposium on Monday, October 16th is a full day event at the UC Davis Conference Center from 9-5pm.

For more information on the agenda, confirmed speakers,

or to register visit:

This morning event on Tuesday, October 17th from 8:30-12pm at the School of Medicine Campus in Sacramento at the Educational Building,

Lecture Hall 2222.

This event will have some of the same speakers as the main campus event, but with more emphasis on medical, health and clinical sciences.

For additional details or to register:


At #UCDavis 10/11 – Sheng Yang He – Microbiome “Disease-Climate-Microbiome” Interactions in the Phyllosphere



Wednesday, October 11

12:10 – 1:00 PM

Life Science 1022

"Disease-Climate-Microbiome" Interactions in the Phyllosphere

Sheng Yang He, Ph.D.
HHMI Investigator
University Distinguished Professor
DOE Plant Research Lab
Michigan State University

Call for Abstracts: 4th Annual UC Davis Human Genomics Symposium

4th Annual UC Davis Human Genomics Symposium

Office of Continuing Medical Education

4th Annual UC Davis
Human Genomics Symposium

Submit Scientific Abstracts
Deadline: Monday, September 18, 2017

Call for Abstracts Flyer

November 17, 2017
Friday, 9am-4pm
UC Davis Education Building, Lecture Hall 1222
4610 X Street, Sacramento, California

Symposium Webpage
Genomic Medicine Webpage

Complimentary Registration

Poster Prizes

University of California, Davis, Health is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians.


UC Davis Health, Office of Continuing Medical Education
4610 X Street #2301, Sacramento, CA 95817