Command-line bootcamp: learn the basics of Unix

Here is another contribution that I made to a UC Davis Bioinformatics Workshop that I helped teach last week. Adapting from some our much longer Unix & Perl Primer for Biologists, I made a short bootcamp that aims to teach the basics of the Unix/Linux command-line.

Unlike the Primer material that was written from the point of view of someone using a Mac, the new bootcamp course is written from the viewpoint of someone using Ubuntu Linux. Also, no example files are needed. The course is entirely self-contained and should take 1–3 hours to process (depending on your familiarity with Unix).

Download the PDF, view the HTML version, or work with the underlying Markdown file.

• Command-line bootcamp (PDF)
• Command-line bootcamp (HTML)
• Command-line bootcamp (Markdown)

Current version: v1.01 — 2015-06-24

Presentation — Genome assembly: the art of trying to make one big thing from millions of very small things

This is an updated version of a talk about genome assembly that I have presented in the past. It is aimed at more of a general audience rather than being about the detailed methods of genome assembly.

Some short slide decks from a recent Bioinformatics Core workshop

Last week I helped teach at a workshop organized by the Bioinformatics Core facility of the UC Davis Genome Center. The workshop was on:

• Using the Linux Command Line for Analysis of High Throughput Sequence Data

I like that the Bioinformatics Core makes all of their workshop documentation available for free, even if you didn't attend the workshop. So have a look at the docs if you want to learn about genome assembly, RNA-Seq, or learning the basics of the Unix command-line (these were just some of the topics covered).

Anyway, I tried making some fun slide decks to kick off some topics. They are included below.

This bioinformatics lesson is brought to you by the letter 'D'

'D' is for 'Default parameters', 'Danger', and 'Documentation

This bioinformatics lesson is brought to you by the letter 'T'

'T' is for 'Text editors', 'Time', and 'Tab-completion'

This bioinformatics lesson is brought to you by the letter 'W'

'W' is for 'Worfklows', 'What?', and 'Why?'

Developments in high throughput sequencing – June 2015 edition →

If you're at all interested in the latest developments in sequencing technology, then you should be following Lex Nederbragt's In beteween lines of code blog. In particular you should always take time to read his annual snapshop overview of how the major players are all faring.

This is the fourth edition of this visualisation…As before, full run throughput in gigabases (billion bases) is plotted against single-end read length for the different sequencing platforms, both on a log scale.

The 2015 update looks interesting because of the addition of a certain new player!