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  • SOlid &&&& Metagenomics

    Are there some research to Metagenomics using Solid???? Otherwise, the short read (about 50bp)to apply thie field????

  • #2
    Are you looking for software, or asking about whether people have used Solid in metagenomics so far ?

    I think de novo assembly is a little trickier, but I'm not worried about the read length for our chosen analysis techniques.

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    • #3
      Originally posted by colindaven View Post
      Are you looking for software, or asking about whether people have used Solid in metagenomics so far ?

      I think de novo assembly is a little trickier, but I'm not worried about the read length for our chosen analysis techniques.
      Thank you for your reply. I want to know whether some papers about Metagenomics on the basic of Solid sequencing.

      Comment


      • #4
        From the website
        Researchers use Applied Biosystems integrated systems for sequencing, flow cytometry, and real-time, digital and end point PCR—from sample prep to data analysis.


        Metagenomics

        Metatranscriptomic analyses of chlorophototrophs of a hot-spring microbial mat
        Publication: The ISME Journal (2011)
        Authors: Liu Z. et al.

        Confirmation of the Sequence of 'Candidatus Liberibacter asiaticus' and Assessment of Microbial Diversity in Huanglongbing-Infected Citrus Phloem Using a Metagenomic Approach
        Publication: Molecular Plant-Microbe Interactions, Vol. 22, No. 12, 2009
        Authors: Tyler et al.

        The carnivorous bladderwort (Utricularia, Lentibulaiceae) a system inflates
        Publication: Journal of Experimental Botany, vol. 61, No1, pp 5-9, 2010
        Authors: Albert, et al.

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        • #5
          In the NCBI SRA there are a couple more studies too, which may not be published:


          1.
          SOLiD sequencing of HLB infected Citrus phloem
          1 ABI_SOLID (AB SOLiD System) run: 337.1M spots, 11.8G bases, 12.2GB downloads
          Accession: SRX004995

          CEG 50-50nt mate-pair library for sample GG3
          1 ABI_SOLID (AB SOLiD System 3.0) run: 315.6M spots, 31.5G bases, 26.1GB downloads
          Accession: SRX105134

          25.
          ABI 50-50nt mate-pair library for sample GG2
          1 ABI_SOLID (AB SOLiD System 3.0) run: 281.8M spots, 27G bases, 22.3GB downloads
          Accession: SRX105133

          26.
          ABI 75nt fragment library for sample GG1
          2 ABI_SOLID (AB SOLiD System 3.0) runs: 339.8M spots, 25.5G bases, 20.7GB downloads
          Accession: SRX105132

          27.
          CEG 35nt fragment library for sample GG1
          1 ABI_SOLID (AB SOLiD System 2.0) run: 171.6M spots, 6G bases, 5.2GB downloads
          Accession: SRX105131

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          • #6
            Thank you for reply. I will try it.

            Comment


            • #7
              The last 4 datasets mentioned are very nice, and are from

              Iverson et al 2012, Science.

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              • #8
                Thanks colindaven, neat papers, esp. genome-from-metagenome one. And yet I still have a question: is it even possible to use raw color-space reads (ie no assembly, no transforming to base space) to analyse a metagenome? As I've heard, BFAST and some other tools can do alignment of .csfasta against reference genome, but will they work against, say, NCBI database?
                Last edited by A_Morozov; 01-21-2013, 10:08 PM. Reason: Just fixing orthography

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