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how to use CLC bio software for assemly with SOLiD

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  • how to use CLC bio software for assemly with SOLiD

    Hello all,
    I am completely new commer to NGS technology and SOLiD platform.
    I want to do de novo assembly of SOLiD data with the CLC bio software
    clc_novo_assmble. apprently this software accepts fastq files for the assembly while I have .csfasta+ qual files. do I need to convert the csfasta+qual to fasq first? do I need to translate it from color space to nt space before doing the assembly?

    Thanks for your help

  • #2
    No, you don't need to convert to fastq if you're using the graphical CLC bio version 4.8+ or probably many earlier versions (I don t know what clc_novo_assmble is!).

    In general, you definitely want to stay in colour space with Solid assemblies if at all possible.


    • #3
      Thank you for your quick answer.

      I will try to use the graphical interface as it is aparently more freindly...
      I tried to use the command line for the novo assembly that is called clc_novo_assemble and it seems like it only accepts fastq files as input while I have csfasta+qual files

      I would have liked to know if someone uses command line clc de novo assembly with color space data ...


      • #4
        Why are you using command line? You can import them in and start the assembly using the GUI interface.