Joint Genome Institute

MGM Workshops

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    • Jan 30, 2023 – Feb 3, 2023

MGM Agenda

Monday

Introduction & IMG Tutorials, Part 1:  Microbial Genome Analysis
Time Title Presenter
08.30–09.00 1. Welcome and Workshop Overview – Nikos Kyrpides
09.00–09.30 2. Introduction to the JGI Science – 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.

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09.30–10.00 3. 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
10.00–10.15 Break – Discussions Continue
10.15–10.45 4. Sequence Assembly Overview – Rob Riley

Genome assembly is the process of inferring the full DNA sequence of a microbial, viral, or eukaryotic chromosome, from many shorter pieces, known as reads.  While the reads produced by current sequencing technologies are getting longer, they still fall short of the full lengths of chromosomes, or even annotatable genomic features such as genes, operons, or biosynthetic gene clusters.  Computational methods for genome assembly are therefore a crucial part of genome sequencing and analysis.  I will give an overview of the theory and practice of genome assembly with applications to both short and long read data.

10.45–11.00 5.Submitting reads to NMDC for assembly [tutorial]– Julia Kelliher

 

11.00–11.30 6. Introduction to IMG – Nikos Kyrpides
12.00–13.00 Lunch & Facility Tour  

 

13.00–13.45 7. Introduction to GOLD – 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.

13.45–14.15 8. IMG Submission & Annotation pipeline [Live Demo] – Marcel Huntemann

 

14.15–14.30 Break – Discussions Continue
14.30–15.15 IMG Navigation I – Nikos Kyrpides
15.15–15.30 IMG Hands-On Exercises I – Users
15.30–16.15 IMG Navigation II – Simon Roux
16.15–16.30 IMG Hands-On Exercises II – Users
16.30–17.00 9. Working Group Formation & Initial Project Discussions – Rekha Seshadri
17.00–19.00 Poster Session & Dinner Reception

Tuesday

IMG Tutorials, Part 2: Microbial Genome Analysis
Time Title Presenter
09.00–09.45 10. 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.

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09.45–10.30 11. 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.

 

10.30–10.45 Break – Discussions Continue
10.45-11.30 IMG Hands On Exercises I – Users user1
11.30-12.00 Exercise I Solutions – Rekha Seshadri
12.00–13.00 Lunch – Discussions Continue
13.00–13.45 IMG Hands On Exercises II – Users user1
13.45-14.15 Exercise II Solutions [Live Demo] – Rekha Seshadri
14.15-14.45 12. Identifying mobile genetic elements with geNomad – Antonio Camargo
14.45-15.00 Break – Discussions Continue
15.00-15.30 IMG/PR – Antonio Camargo
15.30-15.45 Exercise Solutions – Antonio Camargo
16.00-17.00 13. Genome Analysis: A test case – Rekha Seshadri
17.00-17.15 Group Photo

Wednesday

IMG Tutorials, Part 3: Metagenome Analysis
Time Title Presenter
09.00-09:45 14. Introduction to Metagenomics and tools in 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.

 

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09.45-10.30 Metagenome-based discovery [Discussion & Live Demo] – Natalia Ivanova nnivanova
10.30–10.45 Break – Discussions Continue
10.45-11.:30 15. Metagenome binning – Neha Varghese
11.30-12.:00 IMG/M Hands-On Exercises  – Neha Varghese
12.00-13.00 Lunch – Discussions Continue
13.00-13.30 IMG/M Hands-On  Solutions – Neha Varghese
13.30-14.00 16.Viral EcoGenomics – Simon Roux
14.00-14.30 17. IMG/VR – Simon Roux
14.30-14.45 VR Exercises – Users
14.45-15.00 Exercise Solutions – Simon Roux
15.00-15.15 Break – Discussions Continue
15.15-17.30 Working Groups – User Groups user groups

Thursday

Working Group Project Discussions
Time Title Presenter
09.00-09.30 18. New Lineages of Life (NeLLi) – Frederik Schulz
09.30-12.00 Working Groups – User Groups          user groups
12.00- 13.00 Lunch Discussions Continue                                                              
13.00-13.30  Introduction to KBase – Elisha Wood-Charlson
13.30-17.30 Working Groups – 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  –  Tanja Woyke Tanja Woyke
12.00-13.00 Lunch – Discussions Continue
13.00-13.30  20. Overview of Microbial Program – Tanja Woyke Tanja Woyke
13.30-14.00 21. SIP Metagenomics Overview – Rex Malmstrom
14.00-14.30 22. Accelerating functional genomics using mass spectrometry – Ben Bowen

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.

14.30-14.45 Break – Discussions Continue
14.45-15.15 23. DNA Synthesis program – Yasuo Yoshikuni yasuo
15.15-15.45 24. The Secondary Metabolism Collaboratory (SMC): JGI’s new portal for biosynthetic gene cluster data and collaborative analysis – Daniel Udwary
15.45-16.00 25. National Microbiome Data Collaborative – Julia Kelliher
16.00-17.00 26. Fungal/Algal Programs and Systems – Sajeet Haridas & Sara Calhoun
17.00 Workshop Adjourns

Access Presentations & exercises here (page requires password).

 

 

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