Go Back   SEQanswers > Literature Watch

Similar Threads
Thread Thread Starter Forum Replies Last Post
Installation of Burrows-Wheeler Alignment Tool (bwa) on Mac MMPE General 11 06-02-2015 05:56 AM
Burrows Wheeler Transform samanta General 4 10-07-2011 07:16 PM
Bowtie: Burrows Wheeler Transform Siva Bioinformatics 3 03-25-2010 09:32 AM
about burrows-wheeler transform henry Bioinformatics 9 09-05-2009 01:40 AM

Thread Tools
Old 01-19-2010, 11:24 PM   #1
Nils Homer
nilshomer's Avatar
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default Fast and accurate long read alignment with Burrows-Wheeler transform.

Fast and accurate long read alignment with Burrows-Wheeler transform.

Bioinformatics. 2010 Jan 15. [Epub ahead of print]

Li H, Durbin R.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.

MOTIVATION: Many programs for aligning short sequencing reads to a reference genome have been developed in the last two years. Most of them are very efficient for short reads but inefficient or not applicable for reads longer than 200bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. RESULTS: We designed and implemented a new algorithm, BWA Smith-Waterman alignment (BWA-SW), to align long sequences up to 1 megabases against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. AVAILABILITY: CONTACT:

PMID: 20080505 [PubMed - as supplied by publisher]
nilshomer is offline   Reply With Quote
Old 01-28-2010, 10:38 PM   #2
--Site Admin--
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358

hahaha...You demolished my duplicate. At least I had a link to the PDF.
ECO is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:09 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO