Workflow Wednesdays – Part 3. Read preprocessing – Read quality control 1. – Running QC tools

19/06/2013

Read quality control tools can provide very useful information about the the success of your sequencing experiment, without the need to run time consuming alignments and variant calls. Based on read length, per base quality, base content and other basic statistics you can find out a lot about your...

Workflow Wednesdays – Part 2. Read preprocessing – File format conversion

12/06/2013

A little bit about the Linux/Unix command line First of all, let me tell you about the working environment I will use for this data analyis series. I have a laptop with a 4 core Intel processor and 2*4G RAM. I use 64-bit Ubuntu (version 13.04 to be exact)....

Bioinformatics for Beginners – How to get NGS data? Part 1. Short reads

10/06/2013

I recently ran into an email on one of the numerous mailing lists I’m subscribed to. The email was written by a student who was desperately looking for NGS data for testing a pipeline. This letter made me realise that finding short read data is probably not an easy...

Flashcard Fridays – Part 1. Comparison of next generation sequencing technologies

07/06/2013

Recommended articles: Article 1. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers – Quail et al. 2012 This is an incredibly useful review about IonTorrent, Illumina and PacBio technologies. The paper was published in 2012, and contains valuable information...

Workflow Wednesdays – Part 1. Introduction, datasets, plans

05/06/2013

We created an in-house training material for new employees a while ago, which contained a single page, very short workflow for bioinformatics analysis tasks we usually do. I thought it would be a great idea, to go through this workflow step-by-step, collect some tools that can be used for...