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  • Genomic Rearrangement Analysis

    Hi,
    I am new to NGS analysis and we have a project for identifying genomic rearrangements. I have gone through several papers and in the recent time there has been a rise in the number of different softwares and algorithms. and now I'm confused, how do I choose which one is better. Apart from the insertion, deletion, inversions and translocations I also need to find amplifications (copy number variation). I was thinking of a combination of softwares for the study. What is everyones opinion. Please give me some guidance.

    Thanks.
    Shruti

  • #2
    This review is a good starting point.

    Comment


    • #3
      They're all decent, but none of them does an amazing job. The overlap is decent--greater than 50-70% between them generally. False positives and low sensitivity are both major issues.

      The best way to find SVs is to design your experiment appropriately. With current technology, a two-part experiment is best. For human, part one is a low-coverage WGS with 2000bp inserts and part two is medium-coverage WGS with 200bp inserts. The best case is where the insert sizes are a tight distribution centered on these values. This combination is more robust to repeat elements than a typical WGS with a single insert size.

      For algorithms, I'm partial to the one I wrote (Breakway), but there are a number of others in common use (see that review for some examples, or check the wiki here).
      Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
      Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
      Projects: U87MG whole genome sequence [Website] [Paper]

      Comment


      • #4
        Thank you all for the feedback.

        I had read the reviews and also some of the papers in which most of them make their own algorithms for SV detection.

        Yes, it could be a 50-60% of overlap depending upon the kind of signatures they are trying to find. Looks like one cannot use just one tool to identify all types. Though I saw that most people use MAQ for the alignment of reads...

        I think you cannot use PEM for study of amplifications. I saw number of algorithms like binary circular segmentation, EWT and SegSeq.. Which one in your opinion would be ideal.

        Comment

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