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
Thanks a lot.