Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • is it possible to analyze NGS data without access to a server????

    Hi everyone,

    Currently I am not affiliated to any institution so I do not have access to any server, but I have access to some 454-NGS data which I would like to analyze to get my hands a bit on this field, as I am completely new in this.

    The initial objective is to look for markers, microsats, but I thought that I could also try to do some assembling of the runs.

    Can any of you give some reccomendations on computer characteristics that I should try to minimum have?? Like RAM, CPU, processor, ...

    I am aware that if I finally run the analysis on a laptop or stationary computer (without access to server) it might take ages. Alternatively, does anyone know if a particular person can hire server space? and how much would that cost??

    I'll be greatly thankful to any suggestions received

  • #2
    While I do not use it myself, several packages (including Galaxy) run on the Amazon cloud. I suggest searching this forum for AWS or Amazon.

    Comment


    • #3
      Galaxy also has a public server. It can be slow for your particular analysis to move through the queue, but it should have the tools you need.

      Galaxy is a community-driven web-based analysis platform for life science research.
      Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

      Comment


      • #4
        How many data do you have? What analysis do you want to do?

        Comment


        • #5
          Until you're dealing with multiple runs worth of data, you're fine on a 'regular' machine, supposing it has a good amount (16+gb) of ram. There are only a few things that won't run on such a machine overnight. If you're just trying to get some hands-on experience 'doing' the analysis, you don't need to be using a massive stack of data, and if you don't like how long your process is taking, you can always just take a subset of it.

          The processing of data doesn't change much (or really at all, most of the time) on the user side when you scale it up. The analysis and results are affected by the changes, however.

          Comment


          • #6
            454 data is small compared to Illumina data. You should be able to analyze it on a desktop computer.

            Comment


            • #7
              I concur with the last couple of posts - there is little that you can't do with a desktop/laptop computer. Even assembly does not take that much memory if you use e g Minia.

              Comment


              • #8
                For microsatellite searching I can highly recommend the QDD algorithm, it doesn't use much in the way of resources and screens out potential multi-copy loci.

                Comment


                • #9
                  Thanks I'll certainly have a look on this

                  Comment

                  Latest Articles

                  Collapse

                  • seqadmin
                    Strategies for Sequencing Challenging Samples
                    by seqadmin


                    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                    03-22-2024, 06:39 AM
                  • seqadmin
                    Techniques and Challenges in Conservation Genomics
                    by seqadmin



                    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                    Avian Conservation
                    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                    03-08-2024, 10:41 AM

                  ad_right_rmr

                  Collapse

                  News

                  Collapse

                  Topics Statistics Last Post
                  Started by seqadmin, 03-27-2024, 06:37 PM
                  0 responses
                  13 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-27-2024, 06:07 PM
                  0 responses
                  11 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-22-2024, 10:03 AM
                  0 responses
                  53 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-21-2024, 07:32 AM
                  0 responses
                  69 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X