Samuele Bovo

Requirements:

1. be able to use a command line.
2. basic knowledge in programming (python/bash; data need to be mined!).
3. basic concepts in statistics (results need to be interpreted!)
4. time to dedicate to the project.

Mining of genome databases for population genomics studies.

• implementation of pipelines for data and meta-data retrieval.
• implementation of pipelines for data and meta data curation.
  

Analysis of NGS sequencing data forpopulation genomics studies

• dealing with genomic data (up to 56Gb per sample; up to 500 samples).
• processing of raw data (quality check and Sequence alignment).
• detection of variant (SNPs, Indels, CNVs, Chromosomal rearrangement).
• filtering of variants. use of variats for population genomics studies.

Analysis of NGS sequencing data for viromics and One Health applications.

• dealing with genomic and transcriptomic data.
• processing of raw data (quality check and Sequence alignment).
• implementation of pipelines for viral sequences detection.

Analysis of genotype data for population genomics studies

• Genome-wide association studies (GWAS) (univariate statistics, multivariate statistics).
• Detection of Runs of homozygosity (ROHs).
• Selection Signature Analyses.
• implementation of machine learning-based pipelines.

Analysis of metabolomics data in pigs

• implementation of pipelines for data curation.
• implementation of pipelines for data analysies (univariate statistics, multivariate statistics, machine learning).
• implementation of pipelines for data annotation.