About this Workshop
The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) is offering a five-day workshop on Microbial Genomics and Metagenomics. This highly hands-on workshop is designed to familiarize users with the Integrated Microbial Genomes & Microbiomes (IMG/M) data and workflows for computational analysis and interpretation of sequence data. IMG/M is a web-based platform that provides access to the wealth of public microbiome sequence data and enables the user to analyze these data with existing bioinformatic methods to bridge the gap from sequence to biology.
Users will complete hands-on exercises involving comparative analysis, visualization and interpretation of genomic and metagenomic datasets. They will apply these workflows to personal user-defined projects and present findings. The workshop also includes brief overviews of sequencing, assembly, metadata curation, annotation, as well as some presentations from JGI’s portfolio of products beyond sequencing such as DNA synthesis, metabolomics, single cell technology, and more.
Learn more about IMG/M’s capabilities by watching our introductory video.
Who this workshop is for
This course is primarily aimed at benchtop or experimental biologists and budding computational biologists that wish to use IMG resources for (meta)genome exploration, comparative genomics and gene discovery.
Attendees are expected to have some basic understanding of microbiology, biochemistry or molecular biology, and computational biology concepts (e.g., multiple sequence alignment, phylogenetic tree construction). More information on these topics can be found in Richardson & Watson (2012) and Sharpton (2014). Although this workshop centers on computational topics, no programming knowledge is required; all exercises will be performed using the IMG web user interface.
If you are primarily interested in fungal or plant and algal genomes, we encourage you to explore JGI’s other dedicated portals, Mycocosm or Phytozome, respectively and inquire for training opportunities through the Fungal and Plant programs. Although IMG integrates a large number of fungal, algal and plant genomes, these are included primarily to support comparative analysis of microbial genomes.
Upcoming IMG Workshops
- IMG workshop in Spain: July 13-17, 2020, Valencia, SPAIN – REGISTRATION HERE
- MGM-31 at Berkeley Lab: September 28 – October 2, 2020. REGISTER HERE.
Upcoming IMG Webinars
- April 14, 2020 – Genome Search – Advanced Search Builder – Search and filter isolate and environmental (meta)genomic datasets using environmental metadata, sequencing attributes, and more. (Apr 14, 2020. 2 PM EST/11 AM PST. Duration: 20+ minutes)
- April 21, 2020 – IMG data export and download – Individual, or bulk download of genome and metagenome data (genes, scaffolds, annotations), export results from search and analysis in Excel. (Apr 21, 2020. 2 PM EST/11 AM PST. Duration 30+ minutes)
- April 28, 2020 – Metagenome Bins – Browse metagenome scaffold bins (a proxy for MAGs) by taxonomy or ecosystem, assess their quality, and more. (Apr 28, 2020. 2 PM EST/11 AM PST. Duration 40+ minutes)
- May 5, 2020 – Data Submission & Management – Overview of IMG annotation pipeline, submitting project and sequence data to GOLD & IMG for annotation, checking submission status, sharing private genomes with colleagues, releasing your data. (May 5, 2020. 2 PM EST/11 AM PST. Duration 40+ minutes)
Workshop Registration Fee
- Registration fees for the five-day course at LBNL:
- $400 – LBNL Staff
- $400 – Student/Postdoc
- $600 – Non-Academic
DOE Joint Genome Institute
1 Cyclotron Road, Berkeley, CA 94720
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