Agenda

1. Welcome and Workshop Overview

Nikos Kyrpides

09:30–10:00

2. Introduction to the JGI

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.

Jim Bristow

10:00–10:45

3. New Sequencing Technologies

JGI's future depends on new sequencing technologies and applications developed based on these technologies. With multiple sequencing platforms available, JGI's 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 JGI's available sequencing applications in genomic research will be discussed.

Feng Chen

10:45–11:00

Break

11:00–12:00

3. Sequence Assembly Overview

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

Alicia Clum

12:00–13:00

Lunch

13:00–13:30

4. Introduction to the JGI Microbial Program

Abstract to be announced.

Tanja Woyke

13:30–14:00

6. Functional Encyclopedia of Bacteria and Archaea (FEBA)

Deciphering the functions encoded by bacterial genomes remains extremely difficult, with around one third of the genes in a typical bacterial genome being of unknown function. This talk will describe FEBA (Functional Encyclopedia of Bacteria and Archaea) a new project at JGI aimed at addressing this problem. The project aims to apply bacterial growth assays, RNA-Seq and transposon mutagenesis and sequencing (TnSeq) to a panel of 50 phylogeneticallly diverse bacteria, with a goal of providing functional descriptions for thousands of previously ‘unknown’ genes.

Matt Blow

14:00–14.30

Break

14.30-15.00

7. JGI technology development facilitating genome sequencing and annotation

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.

Chia-Lin Wei

15.00-15.30

8. Gene Calling & QA

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.

Amrita Pati

15:30–16:15

9. Data Sources/Annotation

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 databases commonly used for genome analysis will be discussed.

Amrita Pati

16:15–17:00

Working Group Formation & Initial Project Discussions

Users are expected to form working groups of 4-5 participants and formulate a genome or metagenome analysis project, on which they will work in the next 2 days using IMG tools. Working groups will summarize the results of their analysis in 15-20 min presentations on Thursday.

Users

17:00–19:00

Poster Session, JGI tours and Dinner Reception

09:00–10:00

10. IMG-GOLD [Live Demo]

Genome Project selection and Metadata curation

Dino Liolios

10:00–10:30

11. IMG Submission [Live Demo]

Genome and metagenome submission to IMG will be discussed

Marcel Huntemann

10:30–10:45

12. IMG Annotation Pipeline

Genome and metagenome submission to IMG will be discussed

Marcel Huntemann

10:45–11:00

Break

11:00–11:30

13. Microbial Earth Project

Nikos Kyrpides

11:30 -12:00

14. Introduction to IMG

Victor Markowitz

12:00–13:00

Lunch

13:00–13:15

15. IMG Genomes [Live Demo]

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, IMG-based comparative analysis of genomes will be presented.  Tools that will be discussed include phylogenetic profiles and occurrences, genome alignment, abundance profiles, and genome clustering.

Nikos Kyrpides

13:15–14:30

16. IMG Genes [Live Demo]

IMG-based comparative analysis of genes and gene families will be presented.  Tools that will be discussed include homology-based and chromosomal context analysis, occurrence profiles.

Jim Tripp

14:30–14:45

Break

14:45–16:15

17. IMG Functions [Live Demo]

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.  The tools discussed include functional closure, function and pathway profiles, and phenotypes.

Natalia Ivanova

16:15 –16:30

Break

16:30–17:00

18. Test Case: Halothermothrix

The methodology and steps to analyze a genome in IMG will be presented with a user case.

Natalia Ivanova

09:00–09:30

19. Introduction to Metagenomics

Metagenomics, the application of high throughput sequencing to environmental samples is an emerging field that is rapidly advancing our understanding of how microbial communities function and evolve. This introductory talk with trace the roots of metagenomics, it's current practice and speculate on future developments in the field

Susannah Tringe

09:30–10:00

20. Introduction to Metagenomes

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

Natalia Ivanova

10:00–10:45

21. IMG Metagenomes: Metagenome Analysis Tools [Live Demo]

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.

Kristin Tennessen / Amrita Pati

10:45–11:00

Break

11:00–11:30

22. Test Case: Kolumbo Volcano Metagenome

The methodology and steps to analyze a metagenome in IMG/M-ER will be presented as a use case scenario.

Natalia Ivanova

11:30–12:00

Q&A

Users

12:00–13:00

Lunch

13:00–16:30

Working Group Project Discussions

Users

16:30–17:00

23. Soil Metagenomics

Soil microbes are responsible for global cycling of carbon and nutrients, but most have never been isolated and their functions are not known. Sequencing of soil metagenomes has been particularly challenging due to the high complexity and diversity of soil microbial communities. Recently JGI has launched ambitious soil metagenomics sequencing projects to tackle this challenge. Examples of ongoing soil metagenomics sequencing projects will be discussed

Janet Jansson

09:00–11:30

Working Group Project Discussions

Users

11:30–12:00

Q & A

Users

12:00–13:00

Lunch

13:00–16:00

Working Group Presentations

Users

16:00–16:30

24. IMG Tutorial "Postmortem"

Victor Markowitz

16:30–17:00

Feedback

Users

09:00–09:45

25. Single Cell Genomics

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

09:45–10:30

26. Expression Data in IMG

New tools for handling and exploring expression data (proteomics – transcriptomics) will be discussed.

Kostas Billis

10:30–10:45

Break

10:45-11:15

27. Accurate Estimation of Microbial Communities Using Pyrotags and itags

In recent years, microbial community surveys using 454 pyrosequencing technology (pyrotags) gained much popularity and is now the method of choice for profiling microbial communities.
It has revealed that the extent of rare microbial populations in several environments, the “rare biosphere”, is orders of magnitude higher than previously thought. As the Illumina sequencing platforms largely surpassed 454 on terms of read quantity and quality, 16S microbial surveys studies are progressively being done on these sequencing platforms (itags), generating more data and lowering the cost of sequencing. However, the large amount of data, and errors associated with the sequencing technology present significant analytical challenges. I will show how sequencing errors can potentially inflate diversity estimates. I will describe PyroTagger – a fast, scalable computational pipeline designed to ensure accurate estimates of microbial diversity. I will also introduce the analysis of 16S rDNA amplicons on Illumina sequencing platform and discuss new possibilities it offers.

Julien Tremblay

11:15-12:15

28. Intro to ARB

ARB is a software package designed to allow the efficient analysis of ribosomal RNA sequences. It incorporates tools for database management, automatic and manual sequence alignment, phylogenetic tree calculation and the design of discriminatory oligonucleotides used as probes (e.g. for fluorescence in situ hybridization) and primers.

Christian Rinke

12:15–13:30

Lunch

13:30–14:30

29. Vista

The VISTA portal (http://genome.lbl.gov/vista) is a comprehensive comparative genomics resource that provides scientists with a single unified framework to generate and download multiple sequence alignments, visualize the results in the context of existing annotations, and analyze comparative results in the search for important sequence signals in alignments. Among the servers for user-submitted sequences are GenomeVISTA, for aligning a sequence (draft or finished) against whole genome assemblies; mVISTA and wgVISTA, for globally aligning sequences of different species up to 10 Mb long; rVISTA, which uses conservation among species to improve prediction of transcription factor binding sites; and Phylo-VISTA, for visualization of multiple alignments with a phylogenetic tree.

14:30-15:15

30. Genomics of Fungi and Other Microbial Eukaryotes

Many genomes of microbial eukaryotes from different taxonomic groups have been sequenced and analyzed at JGI. The complex exon-intron gene structure makes gene prediction in eukaryotes challenging and requires combination of gene predictors with experimental data and comparative genomics tools. The most significant success in genome sequencing and analysis has been achieved for the Kingdom Fungi, where JGI contributes more than half of genome projects worldwide. The two JGI initiatives, the Genomic Encyclopedia of Fungi and the 1000 Fungal Genomes, aim, respectively, to explore groups of fungi relevant to energy and environment and the fungal diversity at large. To make genome  analysis efficient, fungal genomic data and tools have been integrated in Mycocosm (http://jgi.doe.gov/fungi), the web-based fungal genome portal,  which includes over 200 fungal genomes and promotes user participation.

Igor Grigoriev

15:15–17:00

31. Mycocosm/ Fungal Portal Tutorial

Alan Kuo

17.00

Workshop Adjourns.