Burrows–Wheeler Transform - BWT in Bioinformatics

BWT in Bioinformatics

The advent of high-throughput sequencing (HTS) techniques at the end of the 2000 decade has led to another application of the Burrows–Wheeler transformation. In HTS, DNA is fragmented into small pieces, of which the first few bases are sequenced, yielding several millions of "reads", each 30 to 500 base pairs ("DNA characters") long. In many experiments, e.g., in ChIP-Seq, the task is now to align these reads to a reference genome, i.e., to the known, nearly complete sequence of the organism in question (which may be up to several billion base pairs long). A number of alignment programs, specialized for this task, were published, which initially relied on hashing (e.g., Eland, SOAP, or Maq). In an effort to reduce the memory requirement for sequence alignment, several alignment programs were developed (Bowtie, BWA, and SOAP2) which use the Burrows–Wheeler transform.

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