Submission information
Submission Number: 50
Submission ID: 76
Submission UUID: cd575f43-d878-4f14-9f3d-cd97f1ab443f
Submission URI: /form/project
Created: Wed, 07/22/2020 - 11:45
Completed: Wed, 07/22/2020 - 12:16
Changed: Mon, 09/09/2024 - 14:14
Remote IP address: 24.34.98.209
Submitted by: Lisa Mangiamele
Language: English
Is draft: No
Webform: Project
| Project Title | Genome Sequencing of the Bornean Rock Frog |
|---|---|
| Program | Northeast |
| Project Image |
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| Tags | big-data (4), genomics (537), bioinformatics (277) |
| Status | Complete |
| Project Leader | Lisa Mangiamele |
| lmangiamele@smith.edu | |
| Mobile Phone | 413-454-1961 |
| Work Phone | 413-585-7028 |
| Mentor(s) | Riccardo Racicot, Rob Harbert |
| Student-facilitator(s) | yaniv kovalski |
| Mentee(s) | |
| Project Description | We are working to sequence the genome of the Bornean Rock Frog, Staurois parvus. This frog uses a novel communication signal called "foot flagging", where it waves its back feet to send messages to other frogs. We currently have 220+GB of PacBio Sequel II genome sequence from an adult male frog. To make this genome a usable, accessible tool this sequence needs to be assembled, polished and annotated. This tool will help us investigate the evolution of new behaviors and how hormones regulate the nervous system. Students working on this project will have the opportunity to work in the exciting field of amphibian genomics. Amphibians are notorious for having large complex genomes that are difficult to sequence and assemble. Due to this, students will have a very in-depth experience troubleshooting many steps of the sequencing and assembly pipeline. To date there have only been 10 frog genomes published, so students will have experience in a emerging field. |
| Project Deliverables | Students working on this project will have the opportunity to work in the exciting field of amphibian genomics. Amphibians are notorious for having large complex genomes that are difficult to sequence and assemble. Due to this, students will have a very in-depth experience troubleshooting many steps of the sequencing and assembly pipeline. To date there have only been 10 frog genomes published, so students will have experience in a emerging field. |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | Can work with any level |
| Mentee Programming Skill Level | |
| Project Institution | Smith College |
| Project Address | 44 College Lane Northampton, Massachusetts. 01063 |
| Anchor Institution | NE-MGHPCC |
| Preferred Start Date | 07/23/2020 |
| Start as soon as possible. | No |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | |
| Launch Presentation | |
| Launch Presentation Date | |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones | |
| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | Once assembled this genome will be published. |
| What will the student learn? | Students will learn: -Genome assembly pipelines using multiple assemblers (WTDBG2, Canu) -Genome polishing -Genome size estimation -Possibly genome annotation |
| What will the mentee learn? | |
| What will the Cyberteam program learn from this project? | Amphibian genomics is a unique field due to the large size and complexity of the genome. This poses challenges other genomics projects may not face. The Cyberteam program will learn about assembling large genomes and troubleshooting in genomics. |
| HPC resources needed to complete this project? | The most computationally expensive assembler we plan to run will generate 10-15 TB of intermediary data and use ~1TB of RAM |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | |
| What is the impact on other disciplines? | |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | |
| Lessons Learned | |
| Overall results |