Joint Genome Institute

MGM Workshops

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    • September 28 – October 2, 2020

MGM Agenda

Monday

Introduction & IMG Tutorials, Part 1:  Microbial Genome Analysis
Time Title Presenter
08.30–09.00 Welcome and Workshop Overview – Nikos Kyrpides nikos_v3
09.00–09.30 1. JGI’s Overview – Axel Visel

The powerful high-throughput DNA sequencing technologies catalyzed by the Human Genome Project, which have contributed to dramatic advances in biomedicine, are now being directed to characterizing the genomes of plants and microbes. Leading this effort is the US Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility that unites the expertise of five national laboratories to advance genomics in support of the DOE mission areas of bioenergy, carbon cycling, and bioremediation.

axel2
09.30–10.15 2. DNA Sequencing – Chris Daum

JGIʼs future depends on new sequencing technologies and applications developed based on these technologies. With multiple sequencing platforms available, JGIʼs R&D team has been aimed to develop sequencing applications based on the strength provided by different platforms. Our areas of development lie in de novo whole genome shotgun sequencing, transcriptome sequencing, and metagenomic sample diversity study. Examples of JGIʼs available sequencing applications in genomic research will be discussed.

 Chris Daum
10.15–10.30 Break
10.30-11.15 3. Sequence Assembly Overview – Brian Bushnell

While the ultimate goals for sequencing projects vary as much as the samples themselves, identifying gene content is a nearly universal goal. Recent work has shown that the lower limit for sequence lengths producing good annotation still exceeds read lengths achievable using next generation sequencing platforms. Therefore, assembly is a common step in analysis pipelines, since it can increase sequence length and reduce complexity via clustering. This talk will provide a high level overview of assembly, and discuss challenges and limitations, especially using next generation sequence data.

 

11.15-12.00 4. Introduction to IMG – Nikos Kyrpides nikos_v3
12.00–13.00 Lunch
13.00-13.45 5. Introduction to GOLD [Live Demo] – Supratim Mukherjee

The Genomes Online Database (GOLD) is data management system that catalogs sequencing projects and their associated metadata from around the world. There are three different sources of projects in GOLD: internal projects from the Department of Energy Joint Genome Institute (DOE JGI) that are entered automatically, external projects entered by GOLD users and projects from public databases such as NCBI. GOLD serves as the entry point for projects submitted for analysis to the IMG data management system and ensures that projects are correctly defined along with their necessary metadata. This presentation will provide an overview of the commonly used GOLD terminologies,  a description of its four-level organization system and a tutorial on how to enter sequencing projects in GOLD.

 

Supratim Mukherjee

13.45-14.15 6. IMG Submission & Annotation Pipeline – Marcel Huntemann mhuntemann
14.15-14.30 Break
14.30-16:00 7. IMG Navigation  [Live Demo] –  Nikos Kyrpides
16.00-16:30 IMG Hands On Exercises – Users user1
16.30-17:00 8. Working Group Formation & Initial Project Discussions – Natalia Ivanova
17.00-19.00 Poster Session & Dinner Reception

Tuesday

IMG Tutorials, Part 2: Microbial Genome Analysis
Time Title Presenter
09.00-09.45 9. Introduction to Annotations, Terms and Definitions – Natalia Ivanova 

Annotation of microbial genomes usually starts with finding the genes coding for stable RNAs (rRNA and tRNA) and protein-coding genes (CDSs). The principles underlying gene prediction in microbial genomes, as well as different implementations of these algorithms and most popular gene finding tools will be discussed.Genome analysis and gene function prediction depends on the comparison of sequences to the existing information stored in databases. They can either be simple repositories of nucleotide or protein sequence, or contain curated information related to the function of the genetic elements. Used in combination, bioinformatics databases constitute the most powerful method for gene function prediction. In this presentation, methods commonly used for functional annotation will be discussed.

 nnivanova
09.45-10.30 10. Introduction to Functional annotation  and comparative genomics for gene discovery 

     [Live Demo] – Rekha Seshadri

Microbial genome data analysis in IMG is set in the comparative context of multiple microbial genomes. IMG allows navigating the microbial genome data space along three key dimensions: genomes (organisms), functions (terms and pathways), and genes. In this section, ways in which users can interact with protein families, function assignments, and pathways in IMG will be presented.

 

Rekha Seshadri

10.30-10.45 Break
10.45-11.30 Hands On Exercises I – Users user1
11.30-12.00 Exercise I solutions [Live Demo] – Rekha Seshadri Rekha Seshadri
12.00–13.00 Lunch & Facility Tour
13.00–13.45 Hands On Exercises II – Users user1
13.45-14.15 Exercise II solutions [Live Demo] – Rekha Seshadri Rekha Seshadri
14.15-15.15 11. Introduction to ANI (demo) & Exercises – Neha Varghese
15.15-15.30 Break
15.30-16.15 Introduction to IMG/ABC – Natalia Ivanova  nnivanova
16.15-17.00 12. Genome Analysis: a test case – Rekha Seshadri  Rekha Seshadri
17.00-17.15 Group Photo

Wednesday

IMG Tutorials, Part 3: Metagenome Analysis
Time Title Presenter
09.00-09:45 13. Introduction to Metagenomics Analysis and tools in IMG (IMG/M) – Natalia Ivanova

The main differences between genomes and metagenomes in terms of data and analysis tools will be reviewed.

A snapshot of microbial community structure can be derived from analysis of metagenomic data. IMG/M methods and tools for establishing the taxonomic identity of community members will be presented along with tools for determining the fine population structure, genetic variation and genome dynamics of the dominant populations. Methods for assessing the diversity and abundance of microbial communities will be discussed.

 

nnivanova

09.45-10.30 Metagenome-based discovery [Discussion & Live Demo] – Natalia Ivanova nnivanova
10.30–10.45 Break
10.45-11.:30 14. IMG/M Hands-On Exercises I & Solutions I – Emiley Eloe-Fadrosh emiley-eloe-fadrosh
11.30-12.:00 IMG/M Hands-On Exercises II  – Emiley Eloe-Fadrosh
12.00-13.00 Lunch
13.00-13.30 IMG/M Hands-On  Solutions II –  Emiley Eloe-Fadrosh emiley-eloe-fadrosh
13.30-14.00 15. Metagenome binning: a case study – Emiley Eloe-Fadrosh

Metagenome binning involves grouping assembled contigs from shotgun metagenomic sequences to deconvolute complex microbial communities. A case study will highlight the utility of binning population genomes from metagenomic data.

emiley-eloe-fadrosh
14.00-14.30 16.Viral EcoGenomics – Simon Roux
14.30-15.15 17. IMG/VR – Simon Roux
15.15-15.30 Break
15.30-17.30 Working Group Project Discussions – User Groups user groups

Thursday

Working Group Project Discussions
Time Title Presenter
09.00-09.30 18. Global Giant Virus Diversity and Putative Host Interactions Through Genome-Resolved Metagenomes 
 – Frederik Schulz                                                           
09.30-12.00 Working Group Project Discussions – User Groups          user groups
12.00- 13.00 Lunch                                                              
13.00-17.00 Working Group Project Discussions – User Groups user groups

Friday

User Presentations, and JGI Technologies
Time Title Presenter
09.00-11.30  Working Group Presentations – User Groups user groups
11.30-12.00 19. JGI User Programs  –  Susannah Tringe

JGIʼs future depends on new sequencing technologies and applications developed based on these technologies. With multiple sequencing platforms available, JGIʼs &D team has been aimed to develop sequencing applications based on the strength provided by different platforms. Our areas of development lie in de novo whole genome shotgun sequencing, transcriptome sequencing, and metagenomic sample diversity study. Examples of JGIʼs available sequencing applications in genomic research will be discussed.

12.00-13.00 Lunch
13.30-13.45  20. Introduction to Single Cell Genomics – Tanja Woyke

The bulk of finished microbial genomes to date are derived from bacteria and archaea that can be readily grown in culture. However, the vast majority of microorganisms on this planet elude current culturing attempts, severely limiting access to their genomes. While various enrichment methods as well as metagenomic approaches have been successfully applied to aid the genome analysis of such uncultured environmental microbes, these methodologies are not suitable for countless community members of interest. Single-cell genomics is an approach that aims to access the genome from an individual microbial cell. The methodology as well as a range of JGI single cell projects will be discussed.

Tanja Woyke
13.45-14.30 21. Accelerating functional genomics using mass spectrometry  – Trent Northen

Microorganisms exhibit complex metabolism and metabolic interactions with their environment, large parts of which remain unknown. Deficiencies in functional annotations of microbial genomes as well as incomplete knowledge of small molecule repertoires (metabolomes) of microorganisms limit the understanding of their metabolism. This talk will introduce mass spectrometry based metabolomics and approaches to link these to microbial genomics. This will include recent work connecting genes to the utilization of specific metabolites in bacteria by profiling metabolite utilization in libraries of mutant strains. Here, untargeted mass spectrometry-based metabolomics was used to identify metabolites utilized by soil microbes. Targeted high-throughput metabolite profiling of spent media of 8042 individual mutant strains was performed to link utilization to specific genes. Using this approach we identified genes of known function as well as those required for the metabolism of ‘novel’ metabolites.

 trent
14.30-14.45 Break
14.45-15.15 22.DNA Synthesis program – Yasuo Yoshikuni yasuo
15.15-16.00 23.Fungal Program, Science and Tools – Sajeet Haridas
16.00-16.30 User Feedback user groups
16.30 Workshop Adjourns

 

Access Presentations and exercises here (page requires password)

 

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