Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Hybrid assembling using PacBioToCA?

    This may be a silly question. I know PacBioToCA can be used to correct PacBio long reads by alignment from, for example, Illumina short reads. Then the corrected PacBio reads can be assembled, for example, by Celera assembler. Is this "hybrid" assembly?
    In this pipeline, illumina reads are only used for error correction, but not used in assembling? Should both PacBio reads and illumina reads be used in Celera for assembling as "hybrid" assembly?

  • #2
    Hybrid in sense that assembly is driven by two technologies.

    There are all sorts of variants of hybrids -- cleaning reads (as you've described), co-assembly, merging independent assemblies made with different technologies & assembling with one technology & correcting the consensus with another -- and mix-and-match of all of those

    Comment


    • #3
      Originally posted by krobison View Post
      Hybrid in sense that assembly is driven by two technologies.

      There are all sorts of variants of hybrids -- cleaning reads (as you've described), co-assembly, merging independent assemblies made with different technologies & assembling with one technology & correcting the consensus with another -- and mix-and-match of all of those
      Thanks. So my follow-up question is: is the pacbiotoca--> celera workflow a good way of "hybrid" assembly? Does it fully use the information from two technologies? As far as I know, this is the only built-in "hybrid assembly" method in PacBio's smrtanalysis pipeline. Is it generally good?

      Comment


      • #4
        PacBioToCA can work well for small assemblies, computation quickly becomes an issue with larger assemblies. Smrtanalysis also includes AHA (A Hybrid Assembler) for scaffolding, but that is also limited by assembly size.

        Comment


        • #5
          Originally posted by rhall View Post
          PacBioToCA can work well for small assemblies, computation quickly becomes an issue with larger assemblies. Smrtanalysis also includes AHA (A Hybrid Assembler) for scaffolding, but that is also limited by assembly size.
          Thanks, Rhall! You've been always helpful to me!
          This should be a small genome. I'm not familiar with AHA. Is it something one can combine with the pacbioToCA-celera pipeline, or is it a parallel pipeline?

          Comment


          • #6
            AHA is a separate scaffolding pipeline, if you have an illumina / 454 assembly <20,000 contigs <160 Mbase you can use PacBio long reads and AHA to scaffold and close gaps in the assembly.
            You could also assembly with PacBioToCA then try scaffolding the resulting assembly with AHA in order to recover any of the sequence that was not in the PacBioToCA assembly due to illumina coverage bias.
            Results from AHA should always be validated by resequencing of raw reads, to check for missassemblies.

            Comment


            • #7
              Another hybrid assembler worth noting is Cerulean

              Download Cerulean: Hybrid Genome Assembler for free. Cerulean Hybrid Genome Assembler v0.1 Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind.


              and PBJelly is another PacBio scaffolder

              Comment


              • #8
                +1 for Cerulean, I have seen some really good results for small assemblies and it is computationally efficient.
                Another option for a small genomes, even if you don't have enough coverage to get great denovo PacBio results, HGAP you will still give reasonable sized assemblies with 35-40x coverage, just very fragmented. You could assemble everything independently and merge the assemblies with something like minimus2.

                Comment


                • #9
                  Thank you guys so much. I'll take a look into Cerulean.

                  Comment


                  • #10
                    SPAdes 3.0 (http://bioinf.spbau.ru/en/spades) includes support for hybrid assemblies from Illumina/IonTorrent+PacBio. Additional information (like old contigs, Sanger reads) can be added as well.

                    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, Yesterday, 06:37 PM
                    0 responses
                    8 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, Yesterday, 06:07 PM
                    0 responses
                    8 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 03-22-2024, 10:03 AM
                    0 responses
                    49 views
                    0 likes
                    Last Post seqadmin  
                    Started by seqadmin, 03-21-2024, 07:32 AM
                    0 responses
                    67 views
                    0 likes
                    Last Post seqadmin  
                    Working...
                    X