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  • Alignment of assembly to reference (nuclear genome) [MUMmer]

    I am trying to align an assembly to the reference. I used MUMmer in order to obtain a .coords file. Here are my steps in the command line.

    1. nucmer --prefix=ref_qry ref.fasta qry.fasta
    2. delta-filter -q ref_qry.delta > ref_qry.filter
    3. show-coords -rcl ref_qry.delta > ref_qry.coords


    How to I obtain 2 FASTA files, one containing the set of sequences that aligns to the reference and one containing the set of non aligned sequences?

    I was told I would have to use "parsing" but I'm not sure how to read the headers in the coords file. The labeling isn't explained anywhere in the manual or google.

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