Joint CAMI-M3 workshop on metagenomic software validation
Workshop Day 1 (Sunday, May 7th) – CAMI 2 Workshop
10:30 to 11:00 Registration & Coffee (Juan Jimenez room 2208)
11:00 to 11:10 CAMI Welcome (STAMP, Charles Carrol room 2203)
(Alice McHardy, Helmholtz Centre for Infection Research)
11:10 to 11:40 CAMI 1 recap and lessons learned
(Alice McHardy, Helmholtz Centre for Infection Research; Alex Sczyrba, Bielefeld University)
11:40 to 12:40 Updates from Hackathon
11:40 to 12:00 “Emerging sequencing technologies”
(Andreas Bremges, Helmholtz Centre for Infection Research)
12:00 to 12:20 “Challenges in evaluating strain level resolution”
(Adrian Fritz, Helmholtz Centre for Infection Research)
12:20 to 12:40 “Binning evaluation as part of analysis pipelines”
(Fernando Meyer, Helmholtz Centre for Infection Research)
12:40 to 13:25 Lunch (Juan Jimenez room 2208)
13:25 to 13:45 “Bioboxes overview and discussion”
(Peter Belmann, Bielefeld University)
13:45 to 16:00 CAMI 2 kick-off
13:45 to 14:00 Short CAMI 2 roadmap
(Alice McHardy)
14:00 to 14:45 CAMI 2 – discussing datasets
(Group discussion)
14:45 to 15:00 Coffee break
(Juan Jimenez room 2208)
15:00 to 16:00 CAMI 2 – discussing challenges and performance metrics
(Group discussion)
16:00 to 17:00 “Perspectives on prediction – keeping the goals in sight”
(CAMI Keynote, Fiona Brinkman, Simon Fraser University)
17:00 to 17:10 Break
17:10 to 17:30 “Supercomputing Resources for Open, Accessible, Reproducible Genomic Analysis”
(Phil Blood, Pittsburgh Supercomputing Center)
17:30 to 18:30 Activities with working groups
(Alex Sczyrba)
18:30 to 20:30 Welcome reception and Poster session (Juan Jimenez room 2208)
Workshop Day 2 (Monday May 8th) – M3
8:30 to 9:00 Registration (STAMP, Colony Ballroom room 2203)
9:00 to 9:10 M3 Welcome
(Todd Treangen, University of Maryland College Park)
9:10 to 10:10 “Identifying the micro from the peta: tales of big data in the micro world”
(M3 Keynote, Nikos Kyrpides, JGI)
10:10 to 10:20 Coffee break
10:20 to 10:50 “Standards for Microbiome and Metagenomic Measurements: Supporting the Commercial Translation of Microbiome Science”
(Scott Jackson, NIST)
10:50 to 12:00 Lightning talk session
10:50 to 11:00 “Enhancing metagenomics classification in Kraken with unique k-mer counts”
(Florian Breitwieser, Johns Hopkins University)
11:00 to 11:10 “MinHash techniques for scalable compositional analyses”
(Sergey Koren, NHGRI/NIH)
11:10 to 11:20 “Past, present and future of metaSPAdes metagenomic assembler”
(Sergey Nurk, Saint-Petersburg State University)
11:20 to 11:25 Q&A
11:25 to 11:35 “Democratizing shotgun metagenomics with leaderboard sequencing”
(John Sanders, University of California San Diego)
11:35 to 11:45 “Strain-Level Discrimination of Shiga Toxin-Producing Escherichia coli in the Spinach Microbiome”
(Susan Leonard, US FDA)
11:45 to 11:55 “Bacterial and viral interactions within the oral cavity of tobacco-users”
(Jess Chopyk, University of Maryland College Park)
11:55 to 12:00 Q&A
12:00 to 12:30 Lunch (provided)
12:30 to 15:00 M3 breakout session: Software tool workshop/hands-on-training
12:30 to 13:30 “Metagenome assembly and validation”
(Mihai Pop, Todd Treangen, University of Maryland College Park)
13:30 to 13:45 Break
13:45 to 15:00 “Phylogenetic methods for taxonomic profiling”
(Siavash Mirarab, University of California San Diego)
15:00 to 15:15 Afternoon coffee & Tea
15:15 to 15:45 “Challenges and recent approaches in viral metagenomics”
(Thomas Rattei, University of Vienna)
15:45 to 16:00 CAMI-M3 Closing Comments
(Alice McHardy, Mihai Pop)