Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 454 metagenmic data assembly

    Our data is 454 pyrosequencing metagenomic data (not 16s rRNA). We need to assembly them together for metagenomic study. Some people suggest I should try the same way as Transcript assembly instead of genome assembly because the gene does not occur uniformly across genomes. What's your suggestions.

    We have newbler, velvet, mira available. Which assembler work the best according to your experience for metagenomic data assembly?

  • #2
    For 454 pyrosequencing metagenomic data, you should use newbler.

    Comment


    • #3
      Metagenomic assembly?

      Newbler is super slow!!

      Mira, isn't great if you barcoded your samples...

      I would try Celera or the NEW META-velvet...

      Comment


      • #4
        Newbler is super slow if you can not use correct parameters.
        for example, "-large" for higher abundance data.

        Comment


        • #5
          It depends on the read length!
          Newbler is a good starting point...

          IS it MDA amplified?

          I use meta-velvet for the short reads under 100 bp,
          CAP3 for the singlets from Newbler
          Mira is good for 454...But

          depends on what you want?

          Comment


          • #6
            Originally posted by raw937 View Post
            It depends on the read length!
            Newbler is a good starting point...

            IS it MDA amplified?

            I use meta-velvet for the short reads under 100 bp,
            CAP3 for the singlets from Newbler
            Mira is good for 454...But

            depends on what you want?

            Do you mean you run newbler first, then run meta-velvet for the reads shorter than 100bp, and cap 3 for singlets. How do you combine them together?


            Also, do you have any suggestion about the metagenomic data cleaning specific to 454?

            Thank you

            Comment


            • #7
              The first thing, I would do is try MG-RAST on your reads.
              PrinSeq-lite is a easy perl script to clean your sequences or you can have MG-RAST do it for you off you SFF files.

              Second,
              Newbler first for your reads.
              The singlets should be assembled with CAP3.

              Meta-velvet is best for illumina reads..

              Let me know what you need scripts etc?
              I have been in analysis hell trying to figure all this out, I GOT it so there is no point for you to have the same problems...

              LET ME KNOW
              RAW937

              Comment


              • #8
                Hi Raw937

                After quality control, I have assembled the data by using newbler 2.5. 50% reads assembled into contigs. Then I tried cap3 by using default parameters, around 50% singletons assembled into contigs. However, those contigs are short. only 5% of them are longer than 900bp. What's your suggestion for the CAP3 parameter? Why you think we should use CAP3 here not other assembler? how about newbler with less stringent parameter? Have you thought of mapping assembly?

                Thank you very much!

                Comment


                • #9
                  assembly

                  I do both newbler first to get the main contigs.
                  Then CAP3 for the singlets from 454.

                  You can map you CAP3 only contigs to you Newbler contigs to validate who is telling the truth.

                  I would get an MG-RAST account it will help you out alot to tell you who, what and how your community functions.

                  Its very fast and you can compare to other metas very easily.

                  I would use prinseq lite perl script to clean, then post your reads...

                  Your in Canada eh?

                  I am at UBC where are you?

                  Thanks
                  Raw937

                  Comment

                  Latest Articles

                  Collapse

                  • 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
                  • seqadmin
                    The Impact of AI in Genomic Medicine
                    by seqadmin



                    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                    02-26-2024, 02:07 PM

                  ad_right_rmr

                  Collapse

                  News

                  Collapse

                  Topics Statistics Last Post
                  Started by seqadmin, 03-14-2024, 06:13 AM
                  0 responses
                  32 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-08-2024, 08:03 AM
                  0 responses
                  71 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-07-2024, 08:13 AM
                  0 responses
                  80 views
                  0 likes
                  Last Post seqadmin  
                  Started by seqadmin, 03-06-2024, 09:51 AM
                  0 responses
                  68 views
                  0 likes
                  Last Post seqadmin  
                  Working...
                  X