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  • De Novo Assembly of Wheat Mitochondrial Genomes

    Hi everyone,
    I will soon be analyzing a large number of wheat and wheat wild relative mitochondrial genomes and wanted to get some advice on assembly and analysis here.

    -Library type: Nextera XT libraries generated from purified organellar DNA samples (not total genomic DNA so we don't have to worry about too much nuclear contamination).

    -Sequencing: MiSeqV3-300bp PE (longer reads should hopefully help with assembly)

    Potential QC and Assembly Options (this is where I would like to get some advice)
    1. FastQC and Trimmomatic to remove adapters and low quality bases
    2. I anticipate the coverage being really high, so subsampling reads for assembly will probably be necessary (http://seqanswers.com/forums/showthread.php?t=46174)
    3. Assembly of "Master Circle" - Geneious, Soap de novo, Velvet, Discovar. These seem like the best options, any suggestions?
    4. Annotation and Repeat Identification: Mitofy, Repeat Modeler, Reputer?



    Also, I would like to detect the smaller subgenomic circles, as well as the master circle, but I am unsure as to the best way to go about that.

    After I assemble a number of different wheat and wild relative genomes, I will be variation between them (heteroplasmy, subgenomic circle variation, etc..). I am thinking BreSeq, Discovar, Samtools, SVDetect, etc.. Any suggestions?

    So if any of you experts out there have any helpful suggestions, I would much appreciate it!

  • #2
    Bump! I'm hoping some assembly experts out there have some good advice!

    Comment

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