Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GenoMax
    replied
    You are going to have to do some experimentation with your cluster since each cluster is setup differently, is likely to have limits on how you use the resources and how much of them are going to be available to you (unless you are the only user).

    See this recent thread about efficient ways of submitting blast jobs. The thread focuses on SGE but if your cluster users a different queue management system then you will need to adjust things accordingly. http://seqanswers.com/forums/showthread.php?t=29251

    Leave a comment:


  • Ciaran
    replied
    RAM usage will be dependent on the database size, so extra RAM will not speed up the computation.

    Multi-threading may help as long as the your blast call is consistent with your resource request.

    I have my reservations however with how well blast implements multi-threading, i generally split my input files and run separate blast calls before catting the output files, this however maybe an artifact of my system set up.

    Ciaran

    Leave a comment:


  • Optimal resource allocation for a heavy BLASTN run?

    Hello,

    I need to run BLASTN (locally) on my institution's cluster. My query contains a million short reads and DB contains an equivalent number of sequences.

    What would make the run go faster? More threads, more RAM or both? What would be a number of cores and ram beyond which no benefits are gained?

    Thanks in advance,

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, 06:54 AM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-14-2024, 07:24 AM
0 responses
17 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-13-2024, 08:58 AM
0 responses
16 views
0 likes
Last Post seqadmin  
Started by seqadmin, 06-12-2024, 02:20 PM
0 responses
17 views
0 likes
Last Post seqadmin  
Working...
X