PhD course
High throughput sequencing of non-model organisms
Course material for bioinformatics data analysis
Alexander Jueterbock
Martin Jakt
HTS home site
Materials
This webpage provides course material for the bioinformatics part of the PhD course High throughput sequencing of non-model organisms. This course runs in 2015 the second year at the University of Nordland (Norway).
After a week in the lab to prepare a genome library that is sequenced on the Ion Torrent PGM, we use the second week to focus on the bioinformatics analysis of the resulting data. This involves 1) an introduction to Unix, 2) trimming and quality control, 3) de novo genome assembly, as well as 4) mapping and variant calling.
All tools, script, and programs that we use are open-source and, thus, freely availabe also after the course finishes. An introduction to Unix is invaluable for bioinformatics data analysis. It allows you to build simple pipelines, quickly extract information from large data files, and to automate processes.
In addition, this page provides two lectures on ‘RAD sequencing’ and ‘Introduction to bioinformatics’, as well as a list of sources and literature that delve deeper into the matter that we touch on in this introductory course.