This is the general syllabus for BINF 6203 — Genomics.

Since genomics technologies and analysis methods change rapidly, we do not typically assign a textbook for the course, relying instead on recent review articles to cover important parts of the Genomics domain. If you would like to have a book that provides an overview in addition to the assigned readings, one possibility is Introduction to Genomics, by Arthur Lesk. It does not align perfectly with the course content but it does provide a reasonable overview of many course topics.

Week	Monday	Wednesday
1	Introduction to Genomics	Genomic Data Repositories — Genbank and SRA Lab 1: SRA access and file conversion
2	Genomic Data Formats and Visualization	Next Gen Sequencing Platforms
3	NGS Data QC Lab 2: FastQC, Fast-X and Trimmomatic	Ab initio genome assembly
4	NGS assembly algorithms Lab 3: de novo assembly with SPAdes	Approaches to whole genome sequencing
5	Reference-based “assembly” Lab 3: reference-based mapping with bowtie2/samtools/etc	Read-mapping algorithms
6	Genome annotation Lab 5: gene annotation with myRAST	Genefinding Algorithms
7	Annotation formats and track manipulation Lab 6: Genome Browsers and Bedtools	MIDTERM
8	Comparative Genomics	Gene Ontology and functional classifications
7	Orthology; content and functional comparison Lab 7: Genome alignment and comparison	Variant calling
8	Human genome variation projects Lab 8: Basic variant calling out of genome data	Haplotyping and linkage disequilibrium
9	Whole Genome association studies	Differential expression analysis Lab 9: RNA-Seq with a reference genome
10	Manipulating transcriptome data	Data normalization Lab 10: RNA-Seq analysis by transcriptome assembly
11	Statistics for gene expression analysis	Pathway and gene set analysis Lab 11: GAGE and Pathview
12	Pathview	Gene regulation Lab 12: ChIP-Seq analysis in CLC Genomics
13	Current topics	Current topics