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  • tjahns
    replied
    Oh and useful refers to using the amosvalidate tool for validation without a reference.

    Leave a comment:


  • tjahns
    replied
    Format for using Amos tools

    The best format would probably be an amos/celera assembler message file. You might want to have a look at what velvet does (which can produce such and .afg-file) in this respect.

    Leave a comment:


  • mchaisso
    replied
    also, let me know what you mean by useful-- it will have impact on some development I do over the next couple of weeks.

    Leave a comment:


  • mchaisso
    replied
    euler-sr -> amos

    If you post a link of what sort of format you want to see, I'll see if I can output that along with an assembly (and supply a converter for finished assemblies).

    -mark

    Leave a comment:


  • tjahns
    started a topic Convert euler-sr output to amos-bank

    Convert euler-sr output to amos-bank

    I'm contemplating using the amos validator to get an impression how useful the euler-sr output really is. But I don't see any obvious way to get the mapping of reads to the generated contig.

    Does anyone here know euler-sr or amos well? I'm sort of stuck because if said mapping is not available I don't think I can construct a usable amos-bank.

    Thanks for any pointers I might have missed.

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