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  • looking for reference-guided genome assembly tools

    Hello, there,

    I got the illumina data from two E coli isolate genomic DNA and try to do the assembly. There are many de novo assemblers around. I just wonder if there are any tools for reference-based assembler since this bacterium has reference deposit.

    Thank you very much for any input!

    C

  • #2
    Velvet has options for reference-guided assembly. See the velvet webpage. I think the module for assembly using a reference is called Columbus, and there is a manual.

    https://www.ebi.ac.uk/~zerbino/velvet





    I'm pretty sure you can also do reference-based assembly with Mira.
    Last edited by mastal; 01-15-2017, 02:40 PM.

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    • #3
      Thank you so much for the information. I will explore those methods.

      C.

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