De Bruijn Graph Tutorials are Here

Dear Readers,

It was lot of work, but finally we managed to get the tutorial section ready for you. At this link, you will find our earlier commentaries on de Bruijn graphs arranged in an easy-to-read manner. Several new sections were added here and there to make the text self-contained. The goal is to present de Bruijn graph-based algorithms in the simplest possible manner, so that bioinformaticians understand the applicability of programs they are using for their data types. Quite often, we read comments about using genome assemblers on transcriptome libraries, as you can see from this recent one from SOAPdenovo mailing list -

Dear Sir/Madam/Dr.,

Good day.

I am currently using SOAPdenovo for transcriptome assembly. The software generated contigs of smallest size 100 bp.

I would like to set the minimum contig size to be 200bp. Is there any option in SOAPdenovo allow me to do so?

What took us so much time to set up the tutorials? Thinking through the text and arranging sections logically was difficult enough, but, we also wanted to set up a framework so that future updates can be done seamlessly. The framework had to be compatible with modern viewers, but we were not keen on pulling data out of mysql databases, as in Drupal or Wordpress. On the other hand, we were very reluctant to write our own css, javascript, etc., because maintaining code is bigger nightmare than writing something new. Finally, we decided to combine minimal amount of php and perl coding with Twitter Bootstrap. Our long-term goal is to phase out Wordpress for this blog and choose a CMS that is easy to integrate with our other projects.

Here is our immediate plan for the tutorial section.

1. We are not happy with the writing of few sections. We will continue to polish the text and improve incomplete sections.

2. After we are satisfied with the text, we will post a software-based Chinese translation and request our Chinese readers interested in volunteering to correct the translation. It is too early to start that process, because the English text is not finalized.

3. After we are done with the current text, we have plans to write on many other exciting topics. Two new tutorial sections -

(i) on advanced assembly concepts, where various interesting algorithms like Bloom filter, digital normalization, k-mer counting, string graph, colored de Bruijn graph, etc,

(ii) on various hardware solutions for bioinformatics

-are partly complete, but we need time to clean up the writing and display here.

How do we support these activities?

We do not get even a Cyprus pound to create these community resources. So, if they are of any help to you, a kind word or two would not hurt :)