Burrows Wheeler Transform

[samanta]

I wrote an introductory post on Burrows Wheeler Transform that powers many efficient search programs such as Bowtie, BWA and SOAP2.

http://www.homolog.us/blogs/2011/10/03/finding-us-in-homolog-us/

We usually do not cover topics that are explained everywhere else, and BWT is over 20 years old - so old that it even has a wiki page. However, I could not find a simple explanation of LF mapping property anywhere. LF mapping is used by search programs to map short reads onto reference sequence.

Is it important to learn how the algorithm works to use Bowtie and BWA? I do not think so, but I enjoy shows like car-talk without ever intending to get under the car

[samanta]

Posted part II -

http://www.homolog.us/blogs/2011/10/05/finding-us-in-homolog-us-part-ii/

I worked out another example, and also explained how the search is really done.

[nilshomer]

Great stuff, is part III going to show the auxiliary data structures for an FM-index (occurrence array etc.)?

[samanta]

Great stuff, is part III going to show the auxiliary data structures for an FM-index (occurrence array etc.)?

Thank you !! Still undecided about where to go next. Everyone wants to know how electricity works, but not operations of three phase, or Y-delta, or AC motor.

[nilshomer]

Thank you !! Still undecided about where to go next. Everyone wants to know how electricity works, but not operations of three phase, or Y-delta, or AC motor.

Ask my dog, named Tesla. Anyhow, I would be happy to contribute as I think it would go a long way to those interested.