Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • leecbaker
    replied
    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.

    Leave a comment:


  • adaptivegenome
    started a topic multithreaded GATK local realignment

    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):



    Any feedback or suggestions would be greatly appreciated. Particularly suggestions for future features and development.

Latest Articles

Collapse

  • seqadmin
    Best Practices for Single-Cell Sequencing Analysis
    by seqadmin



    While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
    06-06-2024, 07:15 AM
  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 07:49 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-20-2024, 07:23 AM
0 responses
14 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-17-2024, 06:54 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
25 views
0 likes
Last Post seqadmin  
Working...
X