Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Combined assembly analysis (short reads + long reads)

    Dear NGS Experts,

    I have a question about combined genome assembly.

    We have 75X Hiseq sequencing of an animal species genome (about 3Gb genome size) together with 50X Pacbio Sequel system, now, we would like to make a combined assembly analysis of these 350Gb data. Anybody knows any tools for this kind of analysis?

    Many thanks.

  • #2
    For reference, cross-posted: https://www.biostars.org/p/187524/

    Comment


    • #3
      Originally posted by GenoMax View Post
      For reference, cross-posted: https://www.biostars.org/p/187524/
      Hi GenoMax, thanks a lot. Exactly, if there is any tool which can use the short reads to correct the error on the long reads, that would be great. Such tools should be very useful for combined assembly analysis.

      Comment


      • #4
        Did you see this link: https://github.com/PacificBioscience...Bio-Long-Reads pacBioToCA is the tool you want.

        Comment


        • #5
          Originally posted by GenoMax View Post
          Did you see this link: https://github.com/PacificBioscience...Bio-Long-Reads pacBioToCA is the tool you want.
          Dear GenoMax, thank you very much, that link is quite useful. There is another problem/situation that the genome is with very high heterozygosity, whether the five hybrid assemblers (pacBioToCA, ECTools, SPAdes, Cerulean, dbg2olc) can deal with such situation?

          Comment


          • #6
            You are not going to know until you try. Sounds to me like someone is going to stay busy for a while. Hope you have access to some beefy compute resources since this is going to take a lot of RAM etc.

            Comment


            • #7
              The term you're looking for is "hybrid assembly".

              Comment


              • #8
                Originally posted by GenoMax View Post
                You are not going to know until you try. Sounds to me like someone is going to stay busy for a while. Hope you have access to some beefy compute resources since this is going to take a lot of RAM etc.
                Right, we will try them all. The enough RAM is always important until the transfer rate of sad can reach at least 5GB/s. Thank you again.

                Comment


                • #9
                  I would suggest engaging with PacBio tech support early for this challenging project. Dr. Hall (rhall) from PacBio participates on this forum and he may be a good resource for hints.

                  If you are getting PacBio data from a sequence provider then be sure to ask for raw data files (*.h5). These would be needed for some of the tools we have discussed.

                  Comment


                  • #10
                    There was a thread floating around here somewhere suggesting that you use PacBio reads for assembly and Illumina reads to do error correction, etc. afterwards.

                    Comment

                    Latest Articles

                    Collapse

                    • 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,”...
                      Yesterday, 01:16 PM
                    • seqadmin
                      Recent Advances in Sequencing Analysis Tools
                      by seqadmin


                      The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
                      05-06-2024, 07:48 AM

                    ad_right_rmr

                    Collapse

                    News

                    Collapse

                    Topics Statistics Last Post
                    Started by seqadmin, Yesterday, 07:15 AM
                    0 responses
                    13 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 05-23-2024, 10:28 AM
                    0 responses
                    17 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 05-23-2024, 07:35 AM
                    0 responses
                    20 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 05-22-2024, 02:06 PM
                    0 responses
                    10 views
                    0 likes
                    Last Post seqadmin  
                    Working...
                    X