The Bioinfomatics Support Unit are running a 2 day “Command-line Bioinformatics” training workshop on November 28th and 29th, 2012.
Many powerful bioinformatics applications do not come packaged with an easy-to-use graphical user interface. Since many people are unfamiliar and uncomfortable with the command-line interface that is necessary to get such applications to work, they are unable to unlock the full potential of the valuable data they are generating. The aim of this course is to enable scientists with no prior exposure to a command-line interface to get up and running with this kind of work, and provide them with the fundamentals to use any command-line application. We will start from the basics (not assuming any prior knowledge), and will move through popular bioinformatics tools such as BLAST, before finishing the 2-day course by tackling many of the tools used in the analysis of next-generation sequencing data.
To book a place on the course, please fill in the booking form. The cost of the course to Newcastle University students/staff is £240.
If you are not a member of the University, you can book the course using the University Web Store. External attendees will pay a premium over the cost to internal participants (attendees from charities, or other academic institutions: £290, attendees from commercial companies: £480).
Course Schedule
Day 1 (28/11/2012)
Morning (9.30 – 12.30)
Unix Basics – What is Unix? What is it good for? An introduction to many basic command-line tools that we’ll build upon in the rest of the course.
Afternoon (13.30 – 16.30/17.00)
BLAST – Have you ever found yourself filling in the BLAST form on the NCBI website over and over? Wondering that there must surely be a better way? There is – command-line BLAST lets you run all of those searches with a single command, and gives you far more flexibility and power than the web app ever will.
Multiple Sequence Alignments - A natural extension from the pairwise alignments of BLAST – how are all those sequences you’ve identified in your search related to one another? In this session we’ll cover tools such as CLUSTAL and MUSCLE.
HMMER - More powerful sequence similarity searches and domain finding with Hidden Markov Models.
Day 2 (29/11/2012)
Morning
Tools for sequence analysis - Most tools for the analysis of Next-Generation Sequencing data are command-line based. While graphical interfaces do exist, the true power of these tools can only be exploited by using them at the command-line, as nature intended. On this second day of the course, we’ll give an introduction to many of the most used tools for NGS analysis, and offer practical examples of their usage.
Afternoon
Tools for sequence analysis – Continued from the morning session.
Cancellations
Cancellations up to 14 days before the course start date will incur a 30 per cent cancellation fee. For later cancellations, or non attendance, the full course fee will be charged.
