This list above is great- I'll just add that the Bioconductor Project (an ecosystem of ~1000 packages for bioinformatics in R) has produced a series of very useful tutorial videos on youtube.

Bioconductor's youtube page is here; their introductory video is here, which is a nice starting point for beginners.

There will be a hands-on epigenetics workshop in December this year.

DNA Methylation Data Analysis - How to use bisulfite-treated sequencing to study DNA methylation

These courses are also nice, but not online. Nevertheless, I heard that they are working on an online workshop platform!

Link: http://www.ecseq.com/training.html

NGS Workshop - A Beginner's Guide to RNA-Seq Data Analysis

(1-5 Feb 2016 in Leipzig, Germany)

Visit: http://www.ecseq.com/workshops/rna-seq_2016-01

Although this is not hard-core Bioinformatics tutorials, Rosalind is a great site to teach noobs like me the basics of bioinformatics.

There is a tree of bioinformatic problems that you have to solve using Python, each with explanations, test datasets etc.

And when you complete an assignment it unlocks harder problems.

http://rosalind.info/problems/tree-view/

De Novo Genome Assembly Using Next-Generation Sequence Data

Understand Genome Assembly and perform it yourself.

When?
8 - 10 February 2016

Where?
Leipzig, Germany

In a nutshell

• Learn the essential computing skills for NGS-based assembly
• Understand assembly algorithms and NGS data formats
• Use de novo assembly tools
• Compare different assemblers and evaluate their results

Find the final agenda of the workshop on its website

Check our upcoming NGS data analysis workshop in Munich!

Link: http://www.ecseq.com/workshops/workshop_2016-03-NGS-Next-Generation-Sequencing-Data-Analysis-A-Practical-Introduction

We at ecSeq have several hands-on bioinformatics NGS courses in 2016:

• June 29 - July 1, 2016: Next-Generation Sequencing Data Analysis: A Practical Introduction (Munich, Germany)

• September 5 - 9, 2016: 2nd Prague Summer School - Next-Gen Seq Data Analysis (Prague, Czech Republic)

• September 21 - 23, 2016: microRNA Analysis Using Next-Generation Sequencing (Berlin, Germany)

• September 21 - 23, 2016: DNA Variant Calling Workshop (Berlin, Germany)

• September 28 - 30, 2016: De Novo Transcriptome Analysis - Assembly and Differential Gene Expression (Leipzig, Germany)

• November 22 - 25, 2016: DNA Methylation Data Analysis (Leipzig, Germany)

Please check our website for more information!

Not specifically for bioinformatics, but the software carpentry courses should be on the list. They are particularly useful for wet-lab people who started or is starting to analyse data and need to learn bash, python, and specially good software design practices. Also the courses are free as in beer and free as in speech.

Hey, for more information please visit, http://avli.com.au/courses

I would recommend bioinformatic training courses offered by Arraygen Technologies.

Please visit the site for more details: http://www.arraygen.com/workshop-training.php.

We are also offering bioinformatic training courses in Berlin. Please have a look at our website: https://www.physalia-courses.org/courses/

I did not read that your post was just referring to free courses. Sorry for that. Instead about the quality of free vs. not free courses I totally agree with A. Domingues. Best.