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Bioinformatic analyses of plant genomes
This project aims at acquiring competences and skills in handling large datesets as well as gaining expertise on using computing resources.
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 offer a choice between three possible master thesis projects that address different aspects of genome analyses: a) _De novo_ assembly, curation, and annotation of plant genomes; b) Production and analysis of Bionano data for delivering whole-genome optical maps; c) Transposable element annotation and studies of genome biology and evolution.
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 offer a choice between three possible master thesis projects that address different aspects of genome analyses: a) _De novo_ assembly, curation, and annotation of plant genomes; b) Production and analysis of Bionano data for delivering whole-genome optical maps; c) Transposable element annotation and studies of genome biology and evolution.
Though different in goal and datasets, the projects aim at acquiring competences and skills in handling large datasets and file formats, as well as gaining expertise on using computing resources. We will apply state of the art software and protocols on sequence data obtained from complex plant genomes.
Though different in goal and datasets, the projects aim at acquiring competences and skills in handling large datasets and file formats, as well as gaining expertise on using computing resources. We will apply state of the art software and protocols on sequence data obtained from complex plant genomes.
The three projects span the whole breadth of a modern genome project: from producing a de novo genome assembly, assessing its quality, to construct chromosome-scale pseudomolecules by adopting complementary technologies. The transposable element analysis will take advantage of available software to identify such sequences and perform genome evolutionary analyses. Once the basic bioinformatics concepts are established, we encourage the student to unleash his/her creativity to develop an innovative research method.
The three projects span the whole breadth of a modern genome project: from producing a de novo genome assembly, assessing its quality, to construct chromosome-scale pseudomolecules by adopting complementary technologies. The transposable element analysis will take advantage of available software to identify such sequences and perform genome evolutionary analyses. Once the basic bioinformatics concepts are established, we encourage the student to unleash his/her creativity to develop an innovative research method.
You will gain experience in different aspects of sequence assembly, annotation, genome evolution, and many more. Each project will introduce and guide the student through modern genomics and computational biology techniques.
You will gain experience in different aspects of sequence assembly, annotation, genome evolution, and many more. Each project will introduce and guide the student through modern genomics and computational biology techniques.
A motivated student with interest in genomics, bioinformatics and evolutionary biology. Knowledge of genetics, molecular biology, as well as basic command line skills are required.
A motivated student with interest in genomics, bioinformatics and evolutionary biology. Knowledge of genetics, molecular biology, as well as basic command line skills are required.
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.