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  • Can't find show-aligns in mummer

    Hi,

    I am trying to use mummer: http://mummer.sourceforge.net/manual/#mappingdraft

    to align a contig to a reference genome using:

    nucmer --prefix=ref_qry ref.fasta qry.fasta

    show-coords -rcl ref_qry.delta > ref_qry.coords

    show-aligns ref_qry.delta refname qryname > ref_qry.aligns

    show-tiling ref_qry.delta > ref_qry.tiling

    I have managed to do the first two commands but at the third, it tells me that 'show-aligns' is not found. 'show-tiling' is found though. I have installed mummer through brew with brew install homebrew/science/mummer. Does anybody know how I can get the show-aligns function?

    ==> Installing mummer from homebrew/science
    ==> Downloading https://homebrew.bintray.com/bottles...er-3.23.sierra.
    Already downloaded: /Users/cr517/Library/Caches/Homebrew/mummer-3.23.sierra.bottle.3.tar.gz
    ==> Pouring mummer-3.23.sierra.bottle.3.tar.gz
    🍺 /usr/local/Cellar/mummer/3.23: 143 files, 6.5MB

    ~ which mummer
    /usr/local/bin/mummer

    3.23 pwd
    /usr/local/Cellar/mummer/3.23
    ➜ 3.23 ls
    ACKNOWLEDGEMENTS combineMUMs nucmer2xfig
    COPYRIGHT delta-filter promer
    ChangeLog dnadiff repeat-match
    INSTALL docs run-mummer1
    INSTALL_RECEIPT.json exact-tandems run-mummer3
    LICENSE gaps scripts
    Makefile mapview show-aligns
    README mgaps show-coords
    annotate mummer show-diff
    aux_bin mummerplot show-snps
    bin nucmer show-tiling


    Thanks a lot.

    C.

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