Workflow Wednesdays – Part 3. Read preprocessing – Trimming

07/08/2013

With “short” reads getting longer and longer, read trimming seems to be more and more useful. In my experience, long reads tend to have a significant quality drop at the read end, regardless of sequencing platform, so it makes sense to trim these low quality parts off.

Omixon Academy: Collection of Recent Editions

05/08/2013

After weeks of hard work, it’s worth stopping for a moment and checking all the editions that have been published as a part of Omixon Academy. We might call it the first mid-semester. Please see all the entries below in the three categories we have been using. Bioinformatics for Beginners:...

Bioinformatics for Beginners – BLAST

05/08/2013

Although BLAST (Basic Local Alignment Search Tool) is not strictly a next generation sequencing tool, I use it regularly for a wide variety of tasks. Here are a few scenarios I use BLAST for:

Flashcard Fridays – How accurate is next generation sequencing?

02/08/2013

As for most unspecific questions, my best answer is “it depends”.* And it depends on a lot of things: the sequencing platform, the experiment design, the lab protocol, the quality of the biological sample, the mood of the lab tech, etc. I could go on and on and on and...

Workflow Wednesdays – Part 3. Read preprocessing – Filtering

31/07/2013

After last weeks post about randomly subsampling fastq files, let’s take a look at a different method for making read files smaller.