SEQanswers

Go Back   SEQanswers > Bioinformatics > Open Genomics Engine Project



Similar Threads
Thread Thread Starter Forum Replies Last Post
Local realignment around indels (454 technology) desmo Bioinformatics 2 05-17-2012 05:31 AM
GATK: VCF file for Local realignment around indels jorge Bioinformatics 2 10-10-2011 11:15 PM
Interpreting Local Realignment results from GATK alma Bioinformatics 0 07-07-2011 02:46 AM
GATK recalibration score and local realignment: what is the first step? m_elena_bioinfo Bioinformatics 0 01-24-2011 02:59 AM
Local realignment using GATK and smra seq_GA Bioinformatics 28 01-17-2011 08:10 AM

Reply
 
Thread Tools
Old 08-14-2012, 04:56 AM   #1
adaptivegenome
Super Moderator
 
Location: US

Join Date: Nov 2009
Posts: 437
Default multithreaded GATK local realignment

We have a preliminary implementation of the local realignment process in GATK 1.X (now its called GATK-lite?).

Running on a single core, our implementation is 5-20% faster (the gain increases with file size). Using the AMD 16-core Opteron processors we get up to 5X speed increase. Our principle bottleneck right now is I/O (which we are resolving with advice from Nils, thanks!). The code should be considered experimental so don't add to your production pipelines just yet.

A stable release should be available in the next week or two when we formally push version 0.2 of OpenGE to GitHub. To use the experimental realignment method, you need to build OpenGE from source (we have not updated binaries yet):

http://www.github.com/adaptivegenome/openge

Any feedback or suggestions would be greatly appreciated. Particularly suggestions for future features and development.
adaptivegenome is offline   Reply With Quote
Old 08-30-2012, 07:46 AM   #2
leecbaker
Junior Member
 
Location: .

Join Date: May 2012
Posts: 8
Default OpenGE 0.2 Release

We're pleased to announce the release of OpenGE 0.2 .

Major highlights include:
* Local realignment function. This function realigns reads near indels, using all reads in the region around the indel to find a better alignment for reads. Functionality should be equivalent to GATK's IndelRealigner, but with quicker execution on multicore machines. Some datasets may be up to 12x faster.
* Added functionality to support traceability. When OpenGE performs any operation on a BAM or SAM file, it adds a record to the header of the file describing the command line options used. To review how a file was generated, you can use the new history command.
* Added the 'compare' command to compare BAM/SAM files, and identify differences.
* Many additional bug fixes.

More details are available in the change log included with the binary downloads, and in the command documentation. Source code is available at the OpenGE Github repository.

We welcome any comments and suggestions about improving OpenGE, either via this forum or via email.
leecbaker is offline   Reply With Quote
Reply

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 11:29 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO