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  • anuragk
    Junior Member
    • Dec 2014
    • 3
    #1

    NGS assembly analysis

    Hello,

    I want to know the tools for NGS assembly analysis. And on what algorithm and programming languages these tools are developed in.
    Tags: None
    • guptavipin142
      Member
      • Mar 2014
      • 12
      #2
      For NGS assembly
      for genomes you can go with abyss
      and for
      Metagenome you can go with Velvet 1.2.10
      both are debruigen denovo assembler

        Comment

        • boetsie
          Senior Member
          • Feb 2010
          • 245
          #3
          I think this paper is a good start to give you an overview of the different stages of assembly, but also about pre and postprocessing;

          Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
          http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003345
          Decoding DNA symbols using next-generation sequencers was a major breakthrough in genomic research. Despite the many advantages of next-generation sequencers, e.g., the high-throughput sequencing rate and relatively low cost of sequencing, the assembly of the reads produced by these sequencers still remains a major challenge. In this review, we address the basic framework of next-generation genome sequence assemblers, which comprises four basic stages: preprocessing filtering, a graph construction process, a graph simplification process, and postprocessing filtering. Here we discuss them as a framework of four stages for data analysis and processing and survey variety of techniques, algorithms, and software tools used during each stage. We also discuss the challenges that face current assemblers in the next-generation environment to determine the current state-of-the-art. We recommend a layered architecture approach for constructing a general assembler that can handle the sequences generated by different sequencing platforms.

            Comment

            • anuragk
              Junior Member
              • Dec 2014
              • 3
              #4
              Thanks for your reply

                Comment

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