Burrows-Wheeler technique/transformation/indexing or Bowtie

[isf-bot]

From fcold...@eagle-i.org on October 05, 2012 13:52:18

** Use the form below to request a new term ** ** Scroll down to see a term request example ** Please indicate the label for the proposed term: Burrows-Wheeler technique/transformation/indexing OR Bowtie Please provide a textual definition (with source): Burrows-Wheeler techniques/transformation/indexing as implemented for short read alignment (e.g. of sequences from an RNA-seq run on Illumina). Burrows-Wheeler transform has also been used long read alignment ( http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2828108/ ).

"Bowtie is an ultrafast, memory-efficient alignment program for aligning short DNA sequence reads to large genomes. For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory footprint of approximately 1.3 gigabytes. Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches. Multiple processor cores can be used simultaneously to achieve even greater alignment speeds." http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690996/ Please add an example of usage for proposed term: Bowtie is a specific implementation of Burrows-Wheeler.

In 'Algorithms used' I was unsure if I should request the specific implementation (Bowtie) or the general method "short read alignment using Burrows-Wheeler," as described by Angel.

Original issue: http://code.google.com/p/eagle-i/issues/detail?id=121

[isf-bot]

From sc...@eagle-i.org on October 30, 2012 14:35:47

I'll handle this one.

Status: Accepted
Owner: sc...@eagle-i.org

[isf-bot]

From sc...@eagle-i.org on January 15, 2013 13:09:10

Submitted to SWO as term request.

Status: Started
Labels: algorithm

[isf-bot]

From sc...@eagle-i.org on January 21, 2013 16:53:14

Will be available in release in early February.

Status: Fixed