| Tuesday (Bioinformatics Lectures) | Thursday (Computational Lectures) | |
| 8/23 & 8/25 | Outline of the course | Getting started; First steps with Unix |
| 8/30 & 9/1 | Introduction to environmental ‘omics | First steps with Unix part 2 |
| 9/6 & 9/8 | Introduction to next-generation sequencing | Introduction to Github; Bash scripting |
| 9/13 & 9/15 | Reference sequence databases; sratools hands-on | Makefiles |
| 9/20 & 9/22 | Quality control; Fastqc and Fastx hands-on | Programming with Perl: Hello, World; Data Shapes; Greeting |
| 9/27 & 9/29 | Metagenomic assembly; MegaHIT hands-on | Introduction to HPC: high performance computing |
| 10/4 & 10/6 | Read recruitment and quantification; Bowtie hands-on | File handling |
| 10/11 & 10/13 | Gene finding; Prodigal hands-on | Palindromes (C_HW5, wc) |
10/18 & 10/20
|
* Computational Lecture today DNA Profiling | Sequence Similarity with Kmers |
| 10/25 & 10/27 | Traditional Sequence alignment and BLAST; Centrifuge hands-on | Intro to vim text editor, Types, Counting things |
| 11/1 & 11/3 | Optimizing assembly, read recruitment, and gene calling; the “Uber” protocol hands-on | * Metagenomics Lecture today Functional Annotation; Uproc hands-on |
| 11/8 & 11/10 | Hidden Markov Models (HMM profiles) and searching for patterns; hmmrsearch hands-on | Parsing delimited text/Feature annotation (uproc) Assignment: C_HW8 common words |
| 11/15 & 11/17 | Profiling contigs; Calculating coverage and detecting single nucleotide variations (SNVs) | Modules and OOP; C_HW8 due; Assignment C_HW9 (objects) |
| 11/22 & 11/24 | Genomic binning; hierarchical clustering; CONCOCT hands-on and Interactive visualization in Anvi’o | – Holiday – |
| 11/29 & 12/1 | Phage therapy and overview of last items for the course | Journal-club presentations |
| 12/6 | Course wrap-up; Journal-club presentations | -Dead Day- |
Schedule