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  • simulating illumina paired end reads

    Hello Ladies and Gents,

    I am currently trying to simulate illumina paired end reads. Here is the situation:

    I have a fasta file containing many DNA fragments of different sizes.
    Now I want to simulate paired end reads for each of this fragments including illumina like read errors.

    Do you know a tool / solution for this routine? Actually I am only hold back by the illumina read errors to include. In case of necessity I could programm the rest by myself.

    Thanks a lot,

    Thomas

  • #2
    Hey Splinter479,

    What is your goal of simulating Illumina paired end reads and the purpose of your experiment. Is it sensible to follow this approach.

    Regards,
    Vishnu.

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    • #3
      There are a number of read simulators out there. I've used Sherman recently, and it works OK. There's also wgsim among many others. There's an old post on Biostars with a number of read simulators that should work.

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      • #4
        I am currently programming a complete pipeline for ddRADseq simulation.
        Last step is to create paired end illumina reads.
        My problem is, that the most simulators produce their own fragments (mostly random from a give genome) to produce paired end reads.
        I like to hand in my own fragments into the tool of cause. I have no use of random fragments.

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