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Implementation of a genome assembly algorithm
This project aims to further implement a strategy to simplify the genome assembly step by partitioning the computation in smaller units.
Our research group studies forage plants and other minor crops, focusing on the characterization of relevant genetic traits and their application to breed new varieties. Part of the group’s research focuses on producing and analyzing genomic datasets (genome, transcriptome sequencing, genotyping by sequencing, …) to tackle applied breeding goals by means of a genomics-based approach. We produced Oxford Nanopore sequencing data for a large and complex plant genome, whose assembly would take months and use large computational resources. By exploiting in an innovative way the biological information present in the read data, we developed a method to overcome such limit.
Our research group studies forage plants and other minor crops, focusing on the characterization of relevant genetic traits and their application to breed new varieties. Part of the group’s research focuses on producing and analyzing genomic datasets (genome, transcriptome sequencing, genotyping by sequencing, …) to tackle applied breeding goals by means of a genomics-based approach. We produced Oxford Nanopore sequencing data for a large and complex plant genome, whose assembly would take months and use large computational resources. By exploiting in an innovative way the biological information present in the read data, we developed a method to overcome such limit.
Our goal is to further implement a strategy to simplify the genome assembly step by partitioning the computation in smaller units. The final product will ideally be an open-access software that runs on multiple types platforms.
Our goal is to further implement a strategy to simplify the genome assembly step by partitioning the computation in smaller units. The final product will ideally be an open-access software that runs on multiple types platforms.
With the main concept of the new assembly method already established, its execution needs to be formalized into an efficient code. The project will integrate existing software with customized scripts for the more specific tasks.
With the main concept of the new assembly method already established, its execution needs to be formalized into an efficient code. The project will integrate existing software with customized scripts for the more specific tasks.
You will gain experience in writing code to optimize computational analyses of biological data. The project will introduce and guide the student to handle modern genomics formats and run software on local servers and high-performance computing facilities.
You will gain experience in writing code to optimize computational analyses of biological data. The project will introduce and guide the student to handle modern genomics formats and run software on local servers and high-performance computing facilities.
A motivated student with interest in (bio)informatics and development of computational methods. Scripting skills are required, knowledge of general biology and genomics concepts are considered a plus.
A motivated student with interest in (bio)informatics and development of computational methods. Scripting skills are required, knowledge of general biology and genomics concepts are considered a plus.
For any questions or more details, please contact Dr. Dario Copetti at dario.copetti@usys.ethz.ch.
For any questions or more details, please contact Dr. Dario Copetti at dario.copetti@usys.ethz.ch.