← Back Quiz 9Quiz 10Metagenomics Final: Friday 12/8 1-3pm

Dates and Learning Objectives	Concept Exploration (Due Tuesdays)	Concept Application (Due Thursdays)
Week 1: Course outline and getting started (8/22 & 8/24)	Reading: A Primer on Metagenomics	Reading: https://swcarpentry.github.io/shell-novice/ A long journey to reproducible results “Ten simple rules for managing high-throughput nucleotide sequencing data” Tidy Data Gitbook “Unix”
Week 2: Introduction to metagenomics (8/29 & 8/31)	Reading: A Primer on Metagenomics M_HW1: The metagenomics dictionary	bash C_HW1: work through command-line examples, email history
Week 3: Applications in metagenomics (9/5 & 9/7)	Reading: Project article M_HW2: Abstract (v1)	Git basics More on bash
Week 4: Sequencing technologies (9/12 & 9/14)	Reading: Review on NGS technologies M_HW3: Abstract (v2)	Make bash https://matthias-endler.de/2017/makefiles/ C_HW2: hello (bash)
Week 5: Sharing and storing data (9/19 & 9/21)	Reading: Article on reference databases M_HW4: Intro (v1)	Finish bash C_HW3: cat-n, head
Week 6: Sequence quality control (9/26 & 9/28)	Reading: Review on QC M_HW5: Intro (v2)	Begin Python hello-py
Week 7: Metagenomic assembly (10/3 & 10/5)	Reading: Review on metagenomic assembly M_HW6: M&M + Results (QC)	Python strings/lists/tuples py-strings
Week 8: Metagenomic co-assembly (10/10 & 10/12)	Reading: Megahit article M_HW7: M&M + Results (assembly)	Reading: Python ch 4 Python dictionaries C_HW6: Genetic variation (Hamming)Quiz 4
Week 9: Gene calling (10/17 & 10/19)	Reading: Prodigal article M_HW8: M&M + Results (Co-assembly)	CSV BioPython
Week 10: Genomic binning (10/24 & 10/26)	Reading: Anvi’o article M_HW9: M&M + Results (gene calling)	Pandas
Week 11: Metagenomic sample coverage (10/31 & 11/2)	Reading: Bowtie article M_HW10: M&M + Results (genomic binning)	Reading: Python ch 13 (databases) C_HW9: Converting to fasta format Quiz 7
Week 12: Species diversity (11/7 & 11/9)	Reading: Review on species diversity + centrifuge article M_HW11: M&M + Results (sample cov.)	Reading: Scipy, Numpy C_HW10: Sequence database Quiz 8
Week 13: Functional annotation (11/14 & 11/16)	Reading: Uproc article M_HW12: M&M + Results (species diversity)	matplotlib, R
Week 14: Comparative metagenomics (11/21 & 11/23)	Reading: Infant gut microbiome M_HW13: M&M + Results (function)	Holiday   –
Week 15: Project Presentations (11/28 & 11/30)	M_HW14: Project Presentations	M_HW14: Project Presentations M_HW15: Discussion and conclusions
Week 16: Course wrap-up (12/5 & Final 12/8)	Course wrap-up and final review