What is Burrows-Wheeler Transform used for?

The Burrows–Wheeler transform is an algorithm used to prepare data for use with data compression techniques such as bzip2. It was invented by Michael Burrows and David Wheeler in 1994 while Burrows was working at DEC Systems Research Center in Palo Alto, California.

How does Burrows-Wheeler Transform work?

The Burrows-Wheeler Transform is a text transformation that takes an input string and produces an output string with a high amount of repeating characters. For example the word “banana” is transformed into “annb$aa” ( the “$” will be explained shortly). This output can be efficiently compressed.

How does BWT work?

The BWT is a data transformation algorithm that restructures data in such a way that the transformed message is more compressible. Technically, it is a lexicographical reversible permutation of the characters of a string.

How do you cite BWA?

If you decide to use bwa-mem, please cite: “Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM.

When was the burrows and Wheeler transform invented?

The Burrows–Wheeler transform is an algorithm used to prepare data for use with data compression techniques such as bzip2. It was invented by Michael Burrows and David Wheeler in 1994 while Burrows was working at DEC Systems Research Center in Palo Alto, California.

How does Burrows Wheeler alignment tool ( BWA ) work?

Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.

How to use Burrows-Wheeler transformed text for search?

Looking at the whole process, it is clear that the relative order of A in the sorted text is the relative order of A in the Burrows-Wheeler transformed text. Of course, the same holds for every character. The First-Last property is the key to using the Burrows-Wheeler transformed text for search. The next section will explain how this is done.

Which is the Burrows-Wheeler transform of gatgcgagagatg?

The previous sketch shows that the Burrows-Wheeler transform of GATGCGAGAGATG is GGGGGGTCAA$TAA, as can be verified below. Before explaining how this will help, let us highlight a fundamental property of the Burrows-Wheeler transformed text.