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.
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Can work with any level
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Smith College
44 College Lane
Northampton, Massachusetts. 01063
NE-MGHPCC
07/23/2020
No
Already behind3Start date is flexible
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Once assembled this genome will be published.
Students will learn:
-Genome assembly pipelines using multiple assemblers (WTDBG2, Canu)
-Genome polishing
-Genome size estimation
-Possibly genome annotation
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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.
The most computationally expensive assembler we plan to run will generate 10-15 TB of intermediary data and use ~1TB of RAM
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