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454 Roche. homopolymer error



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  • 454 Roche. homopolymer error

    Hi Everybody,
    I'm currently working on 454 sequencing data generated by roche. I would like to correct homopolymer errors (indels). Do you have a software to recommend me?

    Thank you very much!

  • #2
    Error corrector for Illummina and Roche/454 able to also fix insertions and deletions


    Below are some comments from its author from my Inbox:

    The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made.

    In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected.

    I did not get to test it (yet).


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