A computational pangenomics course and virtual conference in Memphis, TN.
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Practical Course Registration Deadline: 15th April 2023
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Selected Participant will be notified by: 20th April 2023
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Payment Deadline: 29th May 2023
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Virtual Conference Registration Deadline: 29th May 2023
University of Tennessee Health Science Center
Mooney Building,
Library, Room 201,
875 Monroe Ave.,
Memphis, TN 38163
United States
→ See the venue on the map
If you stay in Downtown, the Medical District, South City, or New Chicago, you can reach the course venue by getting on-demand, convenient, and affordable rides with Groove On-Demand.
Tuesday, May 30, 2023 - Thursday, June 1, 2023
The use of a single reference genome in bioinformatics can lead to reference bias and miss important information about genome variability and relationships. New assembly methods have made it easier to generate high-quality complete genome assemblies, and using a pangenome graph that expresses many genomes and their mutual alignment can help address these issues. This course will focus on building such graphs from whole genome assemblies and using them in various downstream applications in comparative genomics, evolution, variation analysis, sequence alignment, and phenotype association.
Participants will learn about pangenome concepts and gain practical experience building and analyzing pangenome graphs. They will apply these methods to complex research questions that require understanding the relationships between multiple genomes or accounting for variability when analyzing new genomes. By the end of the course, participants will have a strong understanding of pangenome methods based on whole genome assemblies.
Friday, June 2, 2023
We will gather for a hybrid in-person and virtual conference on the last day of the week.
This will bring together course participants and virtual and in-person speakers who are actively working on diverse aspects of pangenome research.
The virtual meeting will be open to the public.
Speakers will cover topics at the intersection of pangenome methods and biology, including a focus on basic methods, data structures, genome assembly, data visualization, and public collaborative pangenome projects.
We expect to draw speakers from a diverse set of species contexts.
Genomicist with a quantitative social science background. I build methods that let us understand the precise relationships between thousands of genomes. In these, the genome is encoded in a graph that may represent a population sample of individuals from the same species, a metagenome, the diploid genome of a single individual, or any other useful collection of sequences.
Computer (bio)scientist dedicated to developing and applying new methods to analyze ever-larger collections of sequences (also called "pangenomes") in the tree of life.
Bioinformatician by training. I am exploring methods to calculate and visualize pangenome graph layouts. These are key steps in pangenome graph construction and analysis pipelines. Cluster-scalable pangenomics is the next step.
I am an active member of the Vertebrate Genomes Project (VGP), Earth Biogenome Project (EBP), Human Pangenome Reference Consortium (HPRC) and the Telomere-to-Telomere consortium (T2T).
My research focuses on a variety of topics in and around computational pangenomics. I am part of VG team.
I have a master degree in Medical Biotechnology from the University of Naples Federico II. Currently, I am a PhD student at the University of Tennessee Health Science Center. I am building the pangenome of model organisms (inbred mice and rats) using a combination of second and third generation sequence data.
Computer scientist also trained in interaction design, with a love for mathematics. I work on tooling for variation graphs using the Rust programming language, with a special interest in visualization, which is currently channeled into my pangenome visualization tool Waragraph.
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Andrea Guarracino, University of Tennessee Health Science Center, Memphis, TN, US
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Erik Garrison, University of Tennessee Health Science Center, Memphis, TN, US
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Flavia Villani, University of Tennessee Health Science Center, Memphis, TN, US
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Jordan M Eizenga, University of California Genomics Institute, Santa Cruz, CA, US
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Pjotr Prins, University of Tennessee Health Science Center, Memphis, TN, US
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Robert Davis, University of Tennessee Health Science Center, Memphis, TN, US
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Robert Williams, University of Tennessee Health Science Center, Memphis, TN, US
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Simon Heumos, University of Tuebingen Quantitative Biology Center, Tuebingen, DE
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Vincenza Colonna, University of Tennessee Health Science Center, Memphis, TN, US
University of Tennessee Health Science Center, Department of Genetics, Genomics and Informatics
College of Medicine, Department of Pediatrics
| Day | Time | Speaker(s) | Topic |
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Tuesday, May 30, 2023 |
14:30-16:00 |
Presentation: Introduction to pangenomics |
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16:00-16:30 |
Everyone |
Coffee break |
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16:30-17:15 |
Everyone |
Practical: HLA & LPA graphs, PGGB |
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17:15-17:30 |
Everyone |
Q&A, Day 1 Survey |
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Wednesday, May 31, 2023 |
09:30-10:00 |
Presentation: Understanding pangenomes |
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10:00-10:30 |
Everyone |
Practical: Human pangenome graph building |
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10:30-11:00 |
Everyone |
Coffee break |
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11:00-12:30 |
Everyone |
Practical: ODGI and community detection |
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12:30-14:30 |
Everyone |
Lunch |
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14:30-15:00 |
Presentation: pangenome openness, nf-co.re/pangenome |
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15:00-16:00 |
Everyone |
Practical: pangenome openness, nf-co.re/pangenome |
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16:00-16:30 |
Everyone |
Coffee break |
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16:30-17:15 |
Everyone |
Practical: pangenome openness, nf-co.re/pangenome |
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17:15-17:30 |
Everyone |
Q&A, Day 2 Survey |
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Thursday, June 1, 2023 |
09:30-10:00 |
Presentation: Read mapping with vg giraffe |
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10:00-10:30 |
Everyone |
Practical: alignment and variant calling |
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10:30-11:00 |
Everyone |
Coffee break |
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11:00-12:30 |
Everyone |
Practical: alignment and variant calling |
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12:30-14:30 |
Everyone |
Lunch |
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14:30-15:00 |
Presentation: State of the art in genome assembly |
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15:00-16:00 |
Everyone |
Practical: T2T assembly problems |
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16:00-16:30 |
Everyone |
Coffee break |
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16:30-17:15 |
Everyone |
Practical: T2T assembly problems |
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17:15-17:30 |
Everyone |
Q&A, Day 3 Survey |
Time: Friday, June 2, 2023
Place: 875 Monroe Ave, Mooney Building, Mooney Library
Zoom link: https://tennesseehipaa.zoom.us/j/92881122014
Recording: https://youtu.be/TaoRZYOOC1Y
| Chair | Time | Talk | Speaker |
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09:20 - 09:30 |
Conference Opening |
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09:30 - 10:00 |
Hidden complex genome rearrangements in the plant pangenome graph |
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10:00 - 10:30 |
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10:30 - 11:00 |
Coffee break |
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11:00 - 11:30 |
Unexpected complexity and abundant structural variation in the pangenomes of birds |
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11:30 - 12:00 |
Building a Pangenome Alignment Index via Recursive Prefix-Free Parsing |
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12:00 - 14:00 |
Lunch |
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14:00 - 14:30 |
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14:30 - 15:00 |
Recent human evolution of complex genome architectures |
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15:00 - 15:10 |
Registration includes access to: all lectures and practical sessions, all course materials.
The cost is intended for the course. The conference is free. We do not expect meals to be included.
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Academic - $200, with financial support if needed
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Industry - $400
This course is intended for biologists and bioinformaticians interested in studying organisms with high genetic diversity or without a reference genome, as well as those involved in comparative genomics and the assembly of pangenomes for any species.
Selection of participants will be based on:
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good knowledge of Linux operating system and basic shell commands. This will be a mandatory prerequisite.
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familiarity with genomics data formats (e.g., FASTA, VCF, BED, …) is a plus.
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impact of the course for the participant and his/her research group.
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stage of the research project: priority will be given to participants with data already available and ready to be analyzed (participants data will not be analyzed during the course).
Fulfillment of these conditions by participants will be assessed through the registration form.
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