Genome Sequencing of the Bornean Rock Frog

Project Title: Genome Sequencing of the Bornean Rock Frog
Program:
Northeast (308)

Project Image: https://support.access-ci.org/system/files/webform/project/76/pnas%20parvus.png
Tags:
big-data (4), genomics (537), bioinformatics (277)

Status: Complete
Project Leader
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Project Leader:
Lisa Mangiamele

Email: lmangiamele@smith.edu
Mobile Phone: 413-454-1961
Work Phone: 413-585-7028

Project Personnel
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Mentor(s):
Riccardo Racicot (427), Rob Harbert (623)

Student-facilitator(s):
yaniv kovalski (611)

Mentee(s):
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Project Information
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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 Information Subsection
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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:
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Student Research Computing Facilitator Profile:
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Mentee Research Computing Profile:
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Student Facilitator Programming Skill Level: Can work with any level
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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
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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?:
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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:
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Final Report
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Lessons Learned:
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