applied_bioinformatics
The repository for the Spring 2019 iteration of Applied Bioinformatics. This semester will focus on teaching bioinformatics to undergrads using Nanopore sequencing to drive course projects.
Rob Harbert, rharbert [at] stonehill [dot] edu
Stonehill College
Course Description:
This course explores the growing field of Bioinformatics through hands-on and project based learning. Students will develop basic computational skills to process common biological data streams including programming in R and/or Python. The class will develop skills through a combination of hands-on tech tutorials, a survey of current bioinformatics literature, and group and individual project development. The course will be hyper-focused around one main technology or research question but will introduce and develop computational skills that are widely transferable across Bioinformatics.
The 2019 spring semester course will focus on generating and analyzing genomic DNA sequence data produced by the Oxford Nanopore MinION device. DNA sequencing is generating massive amounts of data that are revolutionizing the way that we do biological research in nearly every area. The MinION is a benchtop, real-time DNA sequencer that is revolutionizing the field of genomics. We will be generating data and exploring bioinformatics tools available to process Nanopore data. Students will work on team and individual research associated with these data.
Learn more about the Oxford Nanopore technology here.
Outline:
Labs/Lectures:
Week 1: Introductions + Computing Basics + Git Setup
Lecture 1: DNA Sequencing Tech
Reading 1 (January 17) The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
A world of opportunities with nanopore sequencing
Week 2: R, RStudio, and RMarkdown
Lecture 2: The Unix Command Line
Reading2 (January 24) Real-Time DNA Sequencing in the Antarctic Dry Valleys Using the Oxford Nanopore Sequencer
Week 3: R and Data Visualization
Lecture 3: Sequence Data Files
Reading 3 (January 31) Nanopore DNA Sequencing and Genome Assembly on the International Space Station
Week 4: Advanced R
Lecture 4: Why Long Reads Matter
Reading 4 (February 7) Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case
Oxford Nanopore Plant Genome White Paper (See eLearn for copy)
Week 5: Nanopore Sequencing
Reading 5 (February 14) From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy
Week 6: Project Proposal Development
Week 6 (February 28) NO READINGS – Project Development Week
Week 7: Spring Break
Week 7 (March 7) NO READINGS – Spring Break
Week 8: Unix and Practical Bash
Lecture 5: NanoPlots – Visualize Sequencing Quality
Week 8 (March 14) NO READINGS – Project Proposal Presentations DUE
Lecture 6: Assembling with Canu
Week 9: Detecting Contamination
Reading 6 (March 21) Nanopore sequencing and assembly of a human genome with ultra-long reads
Week 10: MinION Sequencing (Attempt ‘n’)
Reading 7 (March 28) Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak
Video: Liana Kafetzopoulou - Metagenomic nanopore sequencing: RNA viruses from lab to field
Week 11: Data Workshop: MinION Sequencing
Reading 8 (April 4) Ultra-deep, long-read nanopore sequencing of mock microbial community standards
Week 12: Data Workshop 2: Assembly viewing and polishing
Reading 9 (April 11) New human gene tally reignites debate
Week 13: Project Workshop + Gene Annotation
Week 13b: Filtering raw reads for plastid genome assembly.
Week 14: Project Presentations
Links to Blogs
Use the RMarkdown template provided here . View template output here .
Student written Blogs: HERE
Links to Projects
Below are links to blog posts demonstrating the bioinformatic workflows for published Nanopore sequencing projects. These are distributed under the same CC-BY4.0 + MIT license that the rest of the site is, please attribute to the author listed on each page and reference this site.
Snake venom transcriptomics using R7.3 cDNA sequencing – With data from: Hargeaves & Mulley, 2015
Sequencing the Arabidopsis thaliana genome from a single nanopore flowcell! – Following data and bioinformatics from: Michael et. al., 2018
License for reuse:
CC-BY 4.0 + MIT for code
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