LGN5835 - Applied Bioinformatics

Credit hours

Instructor
Gabriel Rodrigues Alves Margarido

Objective
This course will offer students a theoretical and practical view of technologies available for high throughput genome sequencing, with emphasis on tools available for data analysis. It will enable
students to apply genotyping and transcriptomic strategies to breeding.

Content
Genomics and Bioinformatics. Modern technologies for DNA sequencing. Pre-processing of nucleotide
sequencing data. Biological sequence alignment. De novo genome sequencing and assembly.
Polymorphism prospection and genotyping: genomic resequencing; sequencing of reduced
representation genomic libraries (GBS and RAD). Functional genomics and transcriptomics. De novo
transcriptome assembly. Differential gene expression. Functional enrichment analysis. Software and platforms to be used include: Bowtie, HISAT, BWA-MEM, IGV, TASSEL-GBS, GATK, FreeBayes, Trinity, R,
R/Bioconductor, edgeR, goseq.

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